Since there's indeed tens of thousands items I think maybe update to 3.0+ might help
It's quite stable nowadays but if possible i recommend to test it on different machine user with the same data but no sync (so not to contaminate your main sync target if things go wrong)
SRC: Slowness and sometimes “the window is not responding” error message - #19 by nonobio
Also it might worth to check for unused or faulty resources with batch tool as well