Each of the HEAVY METAL BattleMech Quirks are physically represented by a piece of specialized equipment in one or more Critical Spaces.
The problem comes up when a save for... let’s say a Griffin, tried to put its new Quirk - the 7-Critical Space “Battle Fist” into an Arm that already had all its Critical Spaces already occupied, thus a Broken Save.
True, but with the pilot skill changes, no one loaded a save mid battle and found all their pilots had no skills. Nothing happened until after the battle was done. Something similar could be done with the mechs. Sure, maybe the build is now illegal, but as mentioned above, shouldn't affect anything until you try to drop into your next battle.
Just like the pilot update stripped your pilots and restored XP, Strip gear off the affected mechs. While making rebuilding those mechs a one time instant and free thing would be ideal, simply giving everyone a one time cash influx could also work.