I'm on BES, too, and everytime I update the OS the old messages go away on my BB. I figure that's just fine as I use Outlook as the primary mail tool and they are all still visible there.
I don't have my Windows PC available at the moment, but as I recall, there's a setting in Desktop Manager - either in email settings or syncronize settings - that re-syncs the BB with the BES and Exchange server and will download all your old messages again. Depending on how much old mail you have, it make take awhile.
cant find that all I see close is in sync and it says use the defaultsync setting for the organizer application on my computer then next to that is says reset configuation