I have about 50 users on an "old" Exchange Server (version 5.0 SP2), and I need to move them to a new server. The problem is that the new server must belong to a different organization and must have a different site name from the old, and also it is running Exchange Server 5.5 (SP2 or maybe 3).
I think the best way to approach this is by using ExMerge to produce .PST files and then import them onto the new server. (I intend to export the recipient list and import them to the new server).
What is the best, cleanest way of conducting the upgrade? If I use EXMERGE, does it destroy the data on the old server?
Your initial instinct is a good one. ExMerge is your best solution here, and for only 50 users, it should be relatively painless.
As to whether or not it will destroy the data on the old server, that's up to you. When you run the ExMerge wizard, it will prompt you through a number of questions, one of which specifies how you want the operation to behave: whether you want it just to make copies of the data or remove it from the old mailboxes, for example.