Sounds like I may be having a similar problem/question.  My customer is running QB2019 and has multiple company files as he has restored from backup on several occasions and it had broken the link in the attach files. 

They populated in the document center but were unreachable.  They also showed as attached to any invoices when looking in their register etc.

I copied all the existing attach folder and txn folders  and placed them in the newly created company folder because it was not existent in the newly restored backup and then repaired the linked documents via the company>repair links option.  When I clicked in the document center all of the files came up and the scans were there, however when looking in the register all file attachments were missing and no longer with the transactions.  Is there something I'm doing wrong, or is there even a way to have to do this?