Yes this has annoyed me, I thought these were the sort of achievements that would be around forever so didn't rush to complete. Had I known they would be removed I would have gone to complete them.
I just googled this and found this thread as I had the exact same issue. Went down to like 22 fps just in the first room where you're sneaking around the guards then as soon as I was in the next bit it went back up to normal.