Yes, one of the computers I was using was a direct clone of the other. Including all of the same software. However, I had cloned my main pc about a year and a half ago and had practically zero issues. But about 6 months ago I started having issues. And It didn't seem to matter what I did I would sometimes not have any problems all week and then sometimes I could "restore" the same file 5 times in the same day.
After "clean" installing windows on my laptop it seemed to fix most of the issues. Every now and again one file won't sync between the two and ill end up opening and saving the old version but that problem is minor compared to before when one drive would just automatically start deleting things.
I would recommend uninstalling and then possibly reinstalling windows. But I don't know why this wasn't an issue for a whole year and why it suddenly started messing up. But a clean install did seem to do the trick for me. Since windows pushes automatic updates they should just go ahead and push automatic clean installs.