I ended up doing what Rhonda suggested. I can't say it was a particularly fun experience - there's a certain amount of finger crossing involved, a lot of dohs!, and it broke parts of my app for a little while. But my updates are live now. So, my users are happy once again.
Brandon, let me know if there is anything I can do to help you test the new Flash app work flow? Before the dual pane stuff + this thread got started I think we were all working well together, offering tips and hints to each other. The frustrations just got the better of us. I know a lot about Flash.. so if you need any help testing anything, just ask.