Claude Cowork 2.9939.2 makes deleted sessions unrecoverable via Code CLI

Claude.ai's Cowork desktop app moved to version 2.9939.2 on September 24, bundling Claude Code 2.1.281 and fixing start failures on Mac and Windows, according to the official changelog at claude.com. Buried in that same entry is a change to how deletion works. Session deletion now also erases the local Claude Code transcript, so running claude --resume against a deleted session no longer reopens it. Before this release, deleting a session in Cowork apparently left the underlying Code transcript intact somewhere on disk, recoverable through the command line even after the session vanished from the app.

That gap mattered because transcripts are the record of what a coding agent actually did: commands run, files touched, prompts given. Anyone using Cowork to manage Claude Code sessions across a team had, until now, a quiet safety net if a session got deleted by accident or by policy. The changelog does not say whether old transcripts created before 2.9939.2 are affected, and it does not describe where transcripts are stored or for how long they persisted previously. Those are gaps the company has not addressed publicly as of September 30.

For a developer or engineering manager, the mechanism is straightforward: deletion in the app now triggers deletion of the matching file on the local machine, closing the resume path that claude --resume depended on. That is a smaller surface area for recovery, which cuts both ways. A manager who wants session history preserved for compliance or incident review now has to export or archive transcripts before deleting anything in Cowork, not after. A developer who wants a clean break, say after a client project ends, gets that break more completely than before.

Policy watchers should note the second change bundled into the same release: new Code-tab sessions now start in Auto mode by default, unless an organization has set autoModeEnabled to false. Auto mode likely changes how much the agent acts without per-step confirmation, though the changelog does not spell out what Auto mode permits that the prior default did not. Combined with the deletion change, the release shifts two defaults in the same direction: more agent autonomy up front, less data retained after the fact. Neither default reversal was framed as a security fix in the changelog language itself.

The open questions are practical ones. Teams running Claude Code through Cowork should check whether autoModeEnabled is set at the organization or workspace level, since the new default applies unless that flag is explicitly false. They should also check whether any internal process assumed deleted Cowork sessions could still be pulled via claude --resume, because that assumption breaks with 2.9939.2. Anyone with a retention or audit obligation tied to agent transcripts needs an export step before deletion, not a recovery step after.

What is confirmed is narrow: the version number, the bundled Code release, the Mac and Windows start-failure fix, and the two behavioral changes around deletion and Auto mode, all dated to the September 24 changelog entry. What is not confirmed is how prior-version transcripts are treated, where transcripts live on disk, and what Auto mode's expanded default actually authorizes an agent to do without a prompt back to the user.