My 2 cents…
I really think the program needs a preferences dialogue. I would handle auto sync sort of like dropbox handles selective sync. Let me pick what gets always synced and if I have the option of setting that preferences for all my computers instead of just the current one even better. Auto unsyc should ignore those choices. Auto unsync is not all that useful if it cancels out the auto sync option. Not having a central way of seeing what is set to auto sync is also something that needs to get fixed.