Ah, I assumed when you said “rebuild” that you meant reconstructing the skeleton.
Also, I checked the reference editor, and the reference is indeed correct after changing it. For some reason, though, this seems to not stay after Maya is closed.
Adding the icon, though, seems to have fixed the random crashing, which is a huge improvement.
On another note, is there a way to ensure things like dynamic chains and jiggle bones loop their animation? I noticed an issue before where they wouldn’t necessarily sync up even if the first and last frames were identical, which makes it hard to loop them.