Even if nobody touches those files for 6 months, I still wouldn't let them disappear for a while. You'll save yourself a lot of potential headaches by replicating these PFs to the 2010 box and simply not making them accessible to the users, if you truly want to phase them out (I bet you can create the PF DB, replicate, then take it offline and get it off the exchange storage, if necessary). Document it thoroughly and keep the PF DB around for the longest retention period on your backups (I'd go with 5 years, myself).
It's CYA at it's finest. If nobody ever needs it, you 'wasted' maybe an hour fiddling with it. If they DO need it, you saved yourself a world of aggrivation. I can't tell you how many times I've been called on to resurrect a 2- or 3-year-old file.
Another alternative would be to pull all the data out & stuff it onto some kind of cheap NAS or offline backup. The idea of having to resurrect that Exchange 2003 server so you can restore the PFs from backup in order to retrieve one file... just sounds ugly.