Since I switched to conflict files, I obviously don’t have this problem. But maybe this relates to the underlying problem: I’ve noticed that the conflict files almost never have any actual conflict. One is correct, and the other is an older version. I don’t know why Sync thinks there is an issue; I believe it has happened in cases where I didn’t edit the file on >1 device.
In the most recent case, on my laptop I made a large number of changes to a large note (updating the timestamp format in a project log). I paused Sync while doing it, tho possibly after having made some of the changes. Everything seems to have synced to my phone just fine, but I got a conflict file from my tablet. The conflict file was an older version, and the one with canonical name was the up to date version. I don’t think I edited the file on my tablet.