If the remote is in good order, you should be able to delete more of the local files (of the backup db, not your actual files that were backed up) if not all of it as it just needs to be listed in Duplicati. A repair at that point should re-create the required local suff according to a test that I did some days ago. Vice versa for remote if local is correct.
For using a VM or whatever, I feel that’s a bit of a waste personally. I did more testing including intentional breaking to a backup on this computer and its still going fine 
One more note, if you didn’t try the canary build yet, you could try that. I’m using a source build with latest github code and backups are running fine for me though can’t guarantee it won’t be a problem. However, someone does state in the above link that canary and a full repair there fixed their problem.
I also did a repair to a db downgrade from source to beta on this other computer by doing the stuff I mention above in this post and it also appears to be working fine. But YMMV.