I had been using KeepassXC to refer to a particular device in my WiFi Access Point sub-directory when my cat decided he wanted to help, jumped on keyboard and by the time I had removed him all the entries in that subdirectory had been deleted.
I have no idea how this happened as I had not been editing an entry but they are all all gone.
The problem is that it is not possible AFAIK to copy and paste database entries between Keepassxc databases.
I had some concerns over the backup age but I knew the WiFi Access Points entries were correct on the backup.
I therefore took a copy of the backup file database, deleted all the entries except those for the WiFi Access Points subdirectory, saved it and then tried to merge the edited backup database with the main database that the cat had damaged.
I had a blue banner telling me the merge had been successful but sadly the subdirectory in main database remained empty.
Your description does not show or detail how you performed the actions you performed.
My KeePassXC is version 2.7.9-bp156.2.6.1 from Update repository of openSUSE Backports.
I just closed my database, copied (drag and drop) to another directory, opened the copy (KeePassXC), deleted the entries in the Recycle Bin from using KeePassXC and closed the database copy.
When I repoened the database, the Recycle Bin was empty (as expected) and the rest of the database appeared to be fine. I then closed the “test” copy and switched back to the “Real” database where the deleted entries were present (as expected) and closed the database.
I reopened the “test” database and performed a “Merge From Database” using the “Real” database as the source. The merge was successful, and the deleted entries were restored (as expected).