The --prefix option is meant to support multiple backups in the same directory, but I’ve found that most people have a hard time keeping things separated, so I recommend that you do not use --prefix if you can avoid it.
The problem when changing the prefix like you did, is that the database stores each filename in the database to guard against changes on the destination. When you rename the files, you trigger this guarding operation.
You can use the repair command to recreate the database, and it will rebuild the local database using the filenames found on the remote destination.
Anything that confuses should be fixed, but I think we should stick to the “do not modify the remote destination” rule.
Yes, that really sounds like a bug, but I think it should not be possible to set an empty prefix as that makes it hard to parse the filenames reliably.