Unzip the backup. Determine the path of the missing files from your running DT. Opportunity those files from the exact same location in the unzipped backup.
Why not use the Timemachine backup?
I was able to successfully get the files from the zip by unzipping and loading the database into DevonThink, copying the files to Global Inbox, and closing the database.
Curiously 4 of the files were in a single group; the fifth one was a false positive–it already had size of 0 bytes prior to DevonThink To Go 3.
What if you restore the entire “database” from TimeMachine WITHOUT overwriting. TimeMachine will put a suffix on the file name so as to not over-write the target. Then open that new database in DEVONthink and move whatever files from the restored (but older) database into where you want them.
that is really interesting, maybe this information helps @eboehnisch to reproduce the error if the same files after restoring with the next sync again become ghost files. so it’s reproducable for you? and not solved by deleting and restoring the ghost files?
You can browse your Time Machine backups via Finder as well. There, you can right-click the database and choose show package contents to get to specific files.