Assuming you made the annotations on another computer, if you haven't yet synced that computer you'd still have the version with the annotations there. You could disconnect it from the internet (e.g., turn off wifi), open Zotero, and save a copy of the file there (e.g., drag the attachment to your desktop), and then add it back after syncing (or make another annotation locally to trigger another conflict resolution dialog).

Note that this should only happen if the file was changed on both sides. If you just annotate a file on one computer, Zotero will sync those annotations to another computer without a conflict.

Hmm, OK, that shouldn't happen. If you see another conflict resolution window that you don't expect to see, we'd want to see a Debug ID for a sync attempt through getting the dialog (after which you should click Cancel).

I'm afraid there's no way to restore an unsynced file without a backup of your Zotero data directory.