I’m not going to say it’s best (especially since it’s causing issues for someone), but we’ve noticed that the auto-cleanup option looks like it does VerifyRemoteList, then runs Repair if it finds it wrong. This is before backup, not after. One current problem report began in forum here and is now in GitHub as an issue here.
Although I mention that, I’m not encouraging its use right now, especially with some possible issues in it…
Thank you. If it fails again, we can resume examining things using logs and other tools mentioned above.