Offlineimap has a 'sync_deletes' flag that defaults to 'yes' in both your local and remote repositories. You can elect to delete locally and keep remote, or delete remotely and keep locally.
See the short comment in the offlineimap configuration file on github:
One point that is not clear is how to flag a message locally to be deleted on the remote, without deleting the message locally. What you probably want to do is delete your messages using the GMail UI using a browser.
Remember to make a backup!
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