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Freedom251 › Blog › AI coding agents

How to recover an AI agent’s workspace after it deletes or corrupts files

By Freedom251 Team · · 11 min read

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Stop the agent first, preserve the damaged state, and identify exactly what changed. Then recover from the narrowest source that contains the version you need: an agent or editor checkpoint, Git history, or a snapshot and recovery control belonging to the affected external service. Check the restored files, commit, and diffs before allowing the agent to continue. No single rollback method covers uncommitted files, shell commands, deployments, and external services at the same time.

1. Stop further damage and preserve evidence

If the agent is still running a destructive request, cancel or stop it where doing so is safe. Do not immediately run a broad reset, delete temporary files, or ask the agent to “fix” the damage. Those actions can overwrite the only copy of useful edits and make it harder to determine what happened.

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In the editor or agent interface, record the request that preceded the failure, the changed-file list, and any checkpoint or rewind point shown for that request. Save relevant terminal output and note commands that may have touched files, databases, deployments, or other services. The Visual Studio Code recovery guide recommends assessing changed files, recent tool calls, terminal output, and external effects before choosing a rollback method (Visual Studio Code’s agent recovery guide).

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  • Stop the agent before it can issue more writes.
  • Do not run cleanup commands or a repository-wide restore yet.
  • Keep the current workspace available until you know which files and edits are worth preserving.
  • Note the approximate time of the destructive request and the first point at which the output diverged from the intended result.

2. Establish the scope and the last good version

Recovery is a comparison problem: you need to know which content is wrong, which later edits are valuable, and where the desired version was saved. Start with the agent’s file-change view or session history, then inspect the repository itself.

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Check repository state

  1. Run git status from the repository root. Separate modified, deleted, renamed, staged, untracked, and ignored files.
  2. Run git diff -- to inspect unstaged edits. For staged edits, run git diff --cached --.
  3. Limit inspection to a suspicious path when the change set is large, for example git diff -- src/app.js.
  4. Compare the current commit with the last known-good reference using git log --oneline -n 10 and, when appropriate, git show <commit>:<path>.

Classify every affected file before restoring anything:

  • Good agent or manual work: edits that must survive.
  • Bad agent work: deletions, overwrites, generated output, or corruption to remove.
  • Unrelated changes: work that should not be touched by the rollback.
  • Never recorded content: untracked or ignored files that have no checkpoint or backup.

The earliest divergence matters. If the agent made a good change and then damaged a different file, restoring the whole workspace to an earlier point would unnecessarily discard the good change. Prefer a file-level or hunk-level recovery when the evidence supports it.

3. Match the recovery source to the data it actually saved

Choose a source only after checking that it captured the needed version. The following distinctions prevent a common mistake: using a file rollback to claim that a deployment or a network-side change was also undone.

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Recovery source Best use What it can miss or cannot undo How to verify
Agent or editor checkpoint Rewind workspace files affected by a known request; some systems also restore chat history. Availability and capture scope vary; checkpoints are temporary. They do not reverse completed terminal commands, network requests, deployments, or external-service changes. Inspect the restored file list, then run git status and git diff.
Git history Restore tracked files from a commit, investigate moved branch references, or locate unreachable objects. Git cannot recreate file contents that were never committed, staged, or otherwise stored as Git objects. A careless reset or restore can discard useful edits. Check git status, git log --oneline -1, and the resulting diff.
Agent-specific rewind Undo file changes captured by a particular agent session when its rewind point is eligible. It requires a rewind point and file tracking. Files changed again by a user may be skipped; large files, very large turns, remote-backed sessions, and busy sessions can be ineligible. Use the preview, review skipped files, and inspect Git status and diffs afterward.
Hosted-workspace snapshot Restore provider-managed volumes when the service has a usable snapshot. Scope and timing depend on the provider and available snapshots; it may roll back more than the damaged project. Confirm the snapshot date, restored volumes, and application-level checks.
Other backups or service history Recover files or external effects outside the workspace and repository. Availability, retention, and coverage are environment-specific. Use the service’s own audit, version, or restore controls and verify the resulting state.

4. Restore an editor or agent checkpoint

In supported Visual Studio Code agent sessions, a checkpoint is created before a request. Navigate to the request before the error in the agent conversation and choose its restore action. The checkpoint restores affected workspace files and chat history, but it is temporary and is not a replacement for Git version control (Visual Studio Code documentation).

Use the smallest checkpoint that fixes the problem

  1. Open the agent conversation and locate the request immediately before the destructive operation.
  2. Review the files associated with that checkpoint and compare them with your current changed-file list.
  3. Restore only when the checkpoint’s scope includes the damaged files and the earlier contents are the version you want.
  4. After restoration, inspect the workspace and Git diff before making new edits.

A checkpoint is a file-and-conversation recovery aid, not a transaction log for the whole computer. If the agent ran rm, changed permissions, sent an API request, pushed a deployment, altered a database, or modified another service, those effects remain until you use the corresponding system’s recovery control. Keep a written list of such actions while reviewing terminal output.

5. Recover tracked files with Git without overwriting good work

Git operations are powerful because they can restore a path from a known commit, but each command has a different scope. Read the diff first and specify paths explicitly.

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Discard an unstaged change for one path

If a tracked file should exactly match the current HEAD and its local change is entirely unwanted, use:

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git restore --source=HEAD -- path/to/file

This replaces that working-tree path with the version in HEAD. It does not recover an untracked file, and it should not be used until you have confirmed that every local edit in the path is disposable.

Restore from a particular known-good commit

When the desired content is in another commit, name that commit and the path:

git restore --source=<known-good-commit> -- path/to/file

Inspect the resulting diff. This writes the recovered content into the working tree; it does not automatically create a commit. Once the file is correct, stage and commit it according to your normal review process.

Separate staged and unstaged mistakes

git restore --staged -- path/to/file removes a path from the index while leaving the working-tree content in place. Use it when the agent staged a change that you want to review before committing. To restore both index and working tree from a commit, specify the source and the relevant paths only after confirming that no good work would be lost. The official git restore documentation describes the available source and staging options.

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Investigate a moved branch or lost commit

If the agent committed changes or moved a branch pointer, inspect the local reference log:

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git reflog

Find the entry that names the branch or HEAD before the unwanted move, then inspect it with git show <reflog-entry>. Do not reset immediately; first identify the commit and preserve any current work. The git reflog reference explains how local reference updates are recorded.

Look for unreachable Git objects

If a commit or blob is no longer reachable from a branch but may still be present in the object database, run an investigative command such as:

git fsck --no-reflogs --unreachable

Review the reported object IDs and inspect candidates with git show <object-id>. Object retention is not permanent, and this method cannot help when the content was never written to Git. See the git fsck documentation for the command’s scope and options.

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When Git is not enough

Files that were untracked, ignored, or created and deleted without being stored in a checkpoint, backup, or Git object may have no repository recovery path. Do not imply that git restore can recreate them. Search the agent checkpoint, editor local history, operating-system backup, or the relevant service’s version history instead.

6. Use an agent-specific rewind when its limits fit

GitHub Copilot CLI provides a rewind workflow for eligible sessions. It requires an existing rewind point and file tracking. The documented behavior restores files the CLI changed, but can skip a file when its current content no longer matches what the CLI last wrote; that skip protects later edits from being silently overwritten. The official instructions are in Canceling a GitHub Copilot CLI operation and rolling back changes and Rolling back changes made during a GitHub Copilot CLI session.

Before confirming a rewind, review its preview and compare the listed paths with your evidence. The documentation lists these capture limits:

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  • Individual files larger than 10 MB are not captured.
  • A turn that changes more than 500 files is not captured.
  • File tracking must be available.
  • Remote-backed or busy sessions are not eligible for rewind.
  • A file whose current content differs from the CLI’s last written content may be skipped.

After the rollback, run git status and inspect both staged and unstaged diffs. A successful rewind of captured files does not prove that shell commands, network operations, deployments, or external resources were reversed.

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7. Treat terminal, deployment, and service effects as separate incidents

Workspace restoration changes files; it does not automatically roll back actions performed outside those files. Build an effects list from terminal history, tool-call logs, CI output, and service audit logs.

Terminal and local-system effects

  • Record commands that removed, moved, generated, encrypted, or changed permissions on files.
  • Check whether a command wrote outside the repository, altered environment files, or changed credentials.
  • Use the affected tool’s own undo, restore, or backup mechanism rather than assuming a file checkpoint covers it.

Network and deployment effects

  • Identify API requests, package publication, database migrations, infrastructure changes, and deployments made during the faulty turn.
  • Use the target service’s release history, migration rollback, object versioning, or audit workflow.
  • Reconcile the external state with the recovered source before redeploying; otherwise a redeployment can reintroduce the wrong files.

Hosted virtual workspaces

For Amazon WorkSpaces Personal, the documented restore procedure can restore root and user volumes from available snapshots. Snapshot date, retention, and volume selection determine what is recovered; this is a service-specific procedure, not a guarantee for every hosted development environment. Follow the provider’s instructions at Restore a WorkSpace in WorkSpaces Personal, and verify the restored workspace before reconnecting automation.

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8. Validate the recovery before the agent resumes

Validation should be a deliberate gate, not a quick glance at one file. Use the acceptance criteria for the project and compare the recovered state with the last known-good reference.

  1. Review the file list. Confirm that every intended deletion, restoration, rename, and generated file is accounted for.
  2. Check repository identity. Run git status and git log --oneline -1; confirm the branch and current commit are expected.
  3. Inspect diffs. Run git diff and, when relevant, git diff --cached. Look for accidental formatting churn, secrets, generated artifacts, and unrelated edits.
  4. Run project checks. Execute the repository’s documented tests, type checks, linters, builds, migrations in a safe environment, or other acceptance checks. Choose checks appropriate to the project rather than assuming one command proves correctness.
  5. Verify external state. Confirm deployments, databases, queues, cloud resources, and credentials match the intended version.
  6. Record the boundary. Tell the agent exactly which files are restored, which changes are intentionally retained, what remains unresolved, and what outcome will count as success.

If validation fails, stop again and narrow the diagnosis. Do not repeatedly restore the entire workspace: compare the failing file or behavior with the checkpoint, commit, and external-state records to determine which layer is wrong.

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9. Recovery decisions for common damage patterns

The agent deleted a tracked file and no later edits matter

Inspect the deletion with git diff -- path/to/file, then restore that path from HEAD or the specific known-good commit. Validate references, tests, and generated outputs before staging the result.

The agent overwrote a file that also contains your good edits

Do not use a whole-file restore blindly. Retrieve the earlier version from a checkpoint or commit, compare it with the current file, and merge only the desired hunks. Keep a copy of the current file while comparing so a mistaken merge is reversible.

The agent changed hundreds of files

Use the session’s change preview and Git’s path-limited diffs to divide the set into intentional and destructive groups. An agent-specific rewind may be unavailable when a single turn exceeds its documented 500-file capture limit, so prepare for file- or commit-level Git recovery instead.

The damaged file is larger than the agent rewind limit

Git, an editor checkpoint, a service history, or a system backup may still contain it. GitHub Copilot CLI’s documented rewind capture excludes individual files over 10 MB, so absence from its rewind preview is not proof that the file is permanently lost.

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The agent ran commands that changed production

First recover the source tree only if that helps establish the intended version. Then use the deployment platform, database, infrastructure, or service’s own rollback and audit controls. A workspace checkpoint cannot undo those completed operations.

The workspace is remote-backed or the session is busy

An agent rewind that requires an eligible local session may not be available. Preserve the current state, inspect Git and service history, and use the recovery mechanism that actually recorded the desired version.

10. Optional command-level snapshots

The bashback project describes taking snapshots of working-tree file side effects around shell commands and undoing them. Treat those capabilities as a vendor description rather than an independent guarantee: check supported platforms, the exact files and operations covered, retention, and restoration behavior before relying on it. A command snapshot is not automatically a backup of databases, deployments, network requests, or files outside its coverage. Details are available in the project’s repository at github.com/trouties/bashback.

11. Make future agent work recoverable

Prevention is mostly about creating a known recovery point and limiting the blast radius of an autonomous request.

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  • Commit a known-good baseline. Before a large task, create a clean or clearly documented commit so tracked files have an unambiguous restore point.
  • Define boundaries. State which directories, services, credentials, deployment targets, and generated files the agent must not change.
  • Write observable acceptance criteria. Specify tests, commands, screenshots, API responses, or file properties that demonstrate success.
  • Review early. Inspect the first meaningful result instead of waiting for the entire task to finish; early review limits the number of dependent edits.
  • Use a plan for risky work. Ask for a proposed sequence and affected-file list before permitting broad edits, migrations, or deployments.
  • Keep permissions appropriate. Use the least access needed in unfamiliar repositories and separate development credentials from production credentials.
  • Preserve service-level backups. Enable snapshots, versioning, release history, and database recovery appropriate to systems the agent can reach.
  • Know the agent’s capture limits. Check whether checkpoints are temporary, which files are tracked, and whether remote or busy sessions are excluded.

The practical rule is simple: use evidence to identify the damaged layer, choose the smallest recovery that contains the desired version, and verify every layer before continuing automation.

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