I am using the german version - so please be a little creative with the interpretation of my posting 
At first: I know what I did wrong but I am not able to correct it. Its also not nessessary.
There is a german program called „Papyrus“ that saves a real lot of Backup-Files. My mistake was (on my way getting a great fan of Devonthink) to import these Papyrus-Files into Devonthink.
Unfortunately all the backups were shown in the database. And so I decided to stay on my old system and save my pap-Files seperately from Devonthink. But before that Papyrus did what I wanted it to do: It saved even more backup-Files - now in the Devonthink directory.
I am just at the beginning of my Devonthink experience. So I said: „Ok, it was a mistake“ and I deleted thoses Backups not with the Devonthink dialog. I just deleted them with the finder.
Now „Überprüfen & Reparieren“ (verify & repair?) brought me 3 errors. 2 of them this automatic repair routine was able to repair. 1 stayed.
I didn’t want to go back to a backup, because it could be that I would losing some newer files.
So I chose: „Neuaufbau der Datenbank“ (rebuild the database?). After that I have 109 missing files.
I can do whatever I want (verify & repair or rebuild again) this error is still be shown.
As for me - I know its just Papyrus-Backups that I deleted and don’t need anymore. I am also not able to copy them back because Papyrus did some backup managament. It stores and deleted backups by itself.
My question: Can anybody help me what I can do? As for me I would like just to stay with the database as it is now. Just want to tell the system: „Forget the error, stay like you are now and let us both be happy “ So what can I do to make Devonthink forget these 109 files that it is missing.
Hope my long posting was understandable. Thanks for help.
Thomas