This wasn’t solving things, it was making them worse. The differing names that you undid used to add a benefit because it made sure you got this sort of error if you connected the wrong drive for your backup. For this error, you might have done a backup to the other drive, switched drives, then gotten this error that this different drive has 6 files missing, because they’re on the other drive. To restate, two drives (is one offsite?) requires two jobs.
The local Duplicati database keeps careful track of what files it thinks should be on the remote drive because it wrote them there (and didn’t delete them). This helps it have confidence that all is well, and it can rely on other information it caches about the destination content. If Duplicati had to look all the time, performance would dive.
EDIT: I’m guessing at exactly how far things have gone, but if it’s one good backup and then this error after the switch to the second drive, the second drive might still be empty. If so, try the first drive and see if backup still works. If so, then set things up as suggested with a second job pointing to the second drive, using a different folder as you had before. If you have actual backup data on both drives already, unconfusing the situation might not be practical, and starting over again with clean backups and destinations may be easiest.