This is no different from ACR.
If you export from ACR to PSD, tweak it, print it, and show it to the customer, and then decide the exposure or white point need to change, you need to go back to ACR and generate it again. If you've upgraded ACR, you may very well get a different PSD.
I agree that this can be an issue (as I said, I ran across it myself), but ACR and Aperture act exactly the same way in this regard.
Personally, I think the raw converters themselves...