I was running into quite a few sync problems and noticed many conflicts piling up. I also noticed a modal window popping up in QB every time a 'changes only' sync occurred, complaining about 'single user feature' or some such even though no windows or records were open in QB.
For whatever reason, QB was acting like some transactions (payroll, etc) were still being accessed/in memory and sync wasn't allowed to do its thing.
I restarted QB, let Method sync fire up and it cleared itself out just fine. So...if you see a bunch of conflicts piling up, try restarted QB first and let Method sync up (full sync too) and things should clear up for you. Don't immediately go trying to fix conflict problems since they are likely intermittent. It sucks there are often times there are false positives WRT method-QB data conflicts that only need another full sync to clear out.
Hope that helps someone in future and prevents any unecessary foul ups with your important QB data