If it’s worth the trouble and some added risk, and the destination is one that allows bulk renames (maybe with appropriate tool), you can do bulk renames then either Repair database after renaming old one, or attempt an advanced maneuver that seemed to work when I tried it with DB Browser for SQLite, where a Remotevolume table search-and-replace made the DB Name columns match the renamed files. Test well.
Or just live with prefixes you have now. Changing folder names is simple. Changing prefix names is tricky. There’s no history of previously used prefixes for the backups. It’s one at a time, and DB must match files.
Sounds like the sync only shows the file names. If it showed more path information, you’d know the folder. Path names can be long, but depending on OS, tools, and scripting, are sometimes quite easy to shorten.