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I suggest to have a less invasive warning, rather than a dialog box popping up and blocking your activities.

Maybe a sign on the toolbar: you could have the "sync" button (which already shows an exclamation mark sometimes) showing something, and/or change color into red, or something along this lines. In this way, the warning is clear, but it does not stop your activities when you decide to ignore it.

What do you think?

cheers
--e.