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I actually did this with an ep45-ud3l and an ep45-ud3p and have had a heck of a time getting them both going again. Basically I have gone from two stable computers to one half working computer and another I can't even get to boot from an ubuntu disk...
If your server doesnt have all the latest windows updates, you could create an iso with all of them and performan an "upgrade" install when you switch to the other mobo. This is effectively a repair installation. Since you're ready to do a fresh install on the other system, just go ahead and do that. An alternative is to use a program like Acronis to backup your system for restore on dissimilar hardware, which effectively reverts the drivers to windows 7 default drivers.