I would recommend you cutover your current BES2.2 to the NEW hardware first, let it run for a while. Once satisfied, upgrade to BES4.1 on the NEW hardware. It is a lot easier.
I believe you just need to move the Notes.INI + "BES" data sub-folder over to the new machine to have it operational. But do verify this with RIM or service provider.
Prior to installing BES4.1, check below for a smooth experience:
Article Title: Checklist for upgrading from BlackBerry Enterprise Server software version 2.2 to 4.1
Article Number: KB10024
Link: BlackBerry Search Results
Note: Make sure that the BlackBerry Enterprise Server software version 2.2 is upgraded with the latest service pack before upgrading to software version 4.1.
All the legacy 2.2 service packs are taken off RIM BlackBerry Download site, you may need to contact RIM (if you have T-Support with them) or your service provider for it.