Dale... is it possible to send me (privately) a copy of the AI artwork file, along with instructions on the type of edit you do in Illustrator that is causing the crash? We've fixed issues related to this in the upcoming Preview 2, but want to confirm if your issue is addressed by them.
Artwork structure changes (add/delete layers, etc.) from the artwork file will trump added/deleted layers you've done in the Puppet panel, but shouldn't override any new handles you added in the Puppet panel. Synchronizing artwork structure changes is tricky, and this was the best way to deal with changes at this time -- do structural changes in the artwork file, and handle changes either in the file or in the Puppet panel. However, if you have a behavior associated with a subpuppet, and the artwork changes (for that subpuppet or some other part of the art hierarchy) but that subpuppet still exists, it shouldn't drop the behavior.
Note that if the subpuppet layer is currently selected in the Puppet panel and then an external artwork change occurs, you might need to deselect/reselect the subpuppet layer to see refreshed content (added/removed handle, applied behaviors, etc.). That's been addressed in Preview 2.
Please let us know if the problems have been addressed in Preview 2. Thanks!