Eduard Metzger: really sorry about this, but I've just done a fresh iPad install from app store (as TestFlight version behind for some reason), and it caused sync issues on Mac. Long-deleted sidebar folders came from the dead, and I had repeated sidebar folders too. Even after a restart on Mac I had some of them.
Jonathan Clark: Thanks for letting me know. I got an idea what that might me.
I think the "delete" events get lost somehow when a device haven't been synced for some time. So deleted or moved notes or folders seem to get duplicated.
Eduard Metzger: I'm going to be in this "didn't sync for a week" situation pretty much every week.
Jon Plummer: One more info I learned recently. The sync goes through well, its the sidebar which doesn't get update properly upon receiving the sync after being stale. The workaround for now: Restart the iOS app.
This should be fixed now. There was a problem where the sync worked but the sidebar didn't initially reflect the updates on iOS. Only after a restart. Reopen this, if you still see the problem!