@Arduino gave the usual recommendation (thanks!) which sometimes works, or sometimes the issue moves to a different version. I don’t think anyone has found a great repair. If desperate, do a Recreate, although on current Beta versions there’s a bug that can make it very slow. Both issues are now “fixed” however they need to be released for those on Beta. It’s being worked on but there are snags to settle.
“Unexpected difference in fileset” test case and code clue #3800 was one reason. Might not be the only, however if you’re on a Beta then it could hit during a compact. You can check job log just before, to see whether a compact ran. Using –no-auto-compact can stop that flavor of the issue but it will waste space.
If you’re willing to run Canary (you can’t get back to past Beta easily, but can go to next when it arrives), then Release: 2.0.4.34 (canary) 2019-11-05 seems pretty solid, except for some Stop and Linux issues. Canary releases are test vehicles, so they get the new features, fixes, and inadvertent breakages first…