I can't find any clear guidance on this one. It does not seem to be a tested scenario.
I found this thread with other people describing similiar problems:
http://social.technet.microsoft.com/Forums/en-CA/exchangesvrdeploy/thread/fd8d20ef-b4bc-4e8e-8c3f-8c598c8016d6From my understanding it should work, as long as you stop all exchange services prior to the upgrade.