i finished the "Come Fly With Me" quest line, went back to the hotel, saved... went off to go do some stuff in real life, got back, and now my saves that were all made after finishing the "come fly with me" quest line crash the game.
Is this related to this quest line?

not only, it is a general problem that in same quests (come fly with me is one of them) casue the corruption of all the following saved games after you enter a particular location at a precise step in the quest.

In CFWM quest it starts when you enter the last time in the bunker to give the last objects to launch the missiles. From that point on all your saves will be corrupted.

Load a save before you enter in the underground bunker and your saves will still works (no other solutions actually available from the makers of the game, or I have call them KILLERS of the game?)

Saw there was a big thread about this on the second page... i should have looked.
As for other saves working... none of them work as it is, 20+ hours down the drain