I suggest you go with AP and let them change the movement to the new version. Although expensive, at least you will be able to count on them in the future. If you decide to keep the movement the same, you might find yourself in the same position again in another 5 years.
While I have no direct experience with AP in the US, I think you can trust the quality of their work and also hold them fully accountable for their work.
Having said all of this, it is kind of ridiculous that AP don't want to repair a watch that I wouldn't even consider vintage. I wonder whether AP in Le Brassus would also decline to repair the movement and opt for a replacement (although my guess is that the service center is following directions for AP Switzerland)...
Regarding the originality of the movement, I wouldn't worry about this too much. Just keep the papers from AP that document the work that was done on the watch. Although yours is a nice watch, I would be very surprised if these watches will become highly collectible.
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