You will need to reinstall windows. You can reinstall over the previous one, but I personally feel this is an unclean approach.
If you have data on the old harddrive that you
must recover, you should install over the OS so it is bootable, back up the data, and start over fresh.
This is why having your OS and Data HD separate is a good idea.
RAID mirroring with two harddrives is a great option as well: before doing critical changes such as changing the motherboard, you can break the mirror and garauntee you have a full backup. If you need to reinstall the OS on one of the drives, you can recover the data off of the mirrored one later. Very convenient.