Well, at least in WE(I'm not sure about the original), pressing shift shows if there's any region with a problematic loyalty. Lowering taxes and moving cheap units and shinobi's should work enough to keep loyalty in all of them.

I've had a few reappearings in the past as well, and big ones among them as well, because lots of regions were owned by the rebels, and they tend to massively join the 'resurrection'. Some other clans seem just too goo in causing their people to revolt, and I'm usually slow in taking rebel regions.(They are no treat to me anyway, so no hurry in destoying them. ) So I experienced this quite frequently.