I had the same problem with the flying fortresses. As soon as a cutscene appears (every time an anti-dragon zone is deactivated), I would die if in dragon mode, with just one hit. My solution was to keep track of when it would deactivate, map quicksave to a keyboard key, save just before shooting the last blue flame thingy, and then drop the ground IMMEDIATELY after taking down the zone. Then I would ALT-F4 (quit the game) and restart. After quickloading, it would resume just fine.
A pain, I know, but the workaround does work.
