You shouldn't have to touch the flex disk at all. I swapped the trans mount about 3 months ago, don't recall any problem removing the bolts. There is also no mention of moving the flex disk in the manual. I recall one deceitful thing that looked like a nut, it was actually MB's hard formed receptable for a bolt mounting that goes in from the opposite side.
Had similar occurence when I reupholstered the seats and tried to separate the seat bottom from seat backs. What I thought was a nut was hard formed metal. Man did I put pressure on it with a ratchet, good thing I lost.
Look again - see if its a bolt going in on the other side.