I had the same symptom as the original poster: โCheck for Modificationsโ suddenly became much slower for me. But the decision made (a large number of non-versions of files) did not help.
I continued to search and experiment, and finally found another solution. In my case, I had the "Properties" checkbox selected in the "Items to display" section of the "Check for Changes" window. By checking this box, he accelerated it by an order of magnitude. I'm happy again.
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