If at all possible, make an image of the set-up before you go blowing anything away.
Making an image gurantees that you can restore everything back to it's original state.
Personally I would create a temporary exchange server, add it into the site, and move all of my users mailboxes to it.
The build the new system and migrate the users over to it.
If you ABSOLUTELY have to blow away the present OS w/o building an intermediary exchange server.
Then at the very least, export of of your users e-mail into their own pst files.
Rememeber, once you build the E2K server, you just can't simply 'restore' a backup to it. Because the backup would come from a different system and exchange does not like that. Especially if they are 2different versions.