Is there any way to fix an "unexpected difference in fileset" error other than deleting?

Comparison is internal. Queries done below:

The storedlist is simple, and expandedlist is complex, but the counts are supposed to be the same. Something went inconsistent, so you got told. Duplicati has many self-checks. This one is doing its job… What needs to happen (IMO) is to track down ways these arise, and find a suitable developer to fix them. There may be time and expertise challenges. Not everybody has the skillsets to work on core algorithms.