So far, the only solutions I have come across include doing a backup of the phone and reformatting it, then re-syncing all of the data. I would like to avoid this -- as far as I'm concerned, I migrated my PC, so the phone should recognize the computer and library tied to iTunes...
A P2V'ed system is not the same as the original source regardless of your concerns and that's just the way it is. 
Basically no different then attempting to sync with to two (or more) separate systems (physical or virtual) and as such you'll have to deal with the inconsistencies created by the P2V'ed system.
I haven't had to deal with it lately as I always sync my iGagets natively with my MacBook Pro however IIRC using Deauthorize this Computer on the source before conversion and then Authorize this Computer on the VM afterwards allowed me to not have to do a wipe and restore.