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Actually, in the absence of any real information, I'm going to take a wild stab in the dark and guess:
You Full Annexed a bunch of New World nations, such as Creek and Inca
You didn't core them yourself, or not all of them
It's just rolled past 11th November 1644
As per the "Disappearing Cores, Full Annex does not reset core timers from game start" bug, still present in 1.3.2, all those cores disappeared, because they had a 200 year timer still starting 1444, not time of annexation as it should be.
That's the Anvil. I basically had conquered all the new world natives. It took a long time to pacify them. I did not bother to core them. And then all hell broke loose about 1644 as you say.
And yes, I did weather the storm. Though it was tiring about about 10 years.