It depends on the CPU? If they are the same architecture (e.g. both Intel, both 64 bit) then you should be ok. I understand that some versions of Windows use a different kernel for single core than for multiple core although that may be less of an issue (I've seen a VM created for 4 cores have 3 cores removed and still run fine).
So if you aren't making a radical change to CPU, and the rest of the server has the same hardware, I think you may be ok. But if the data is valuable at all, be sure to backup before trying this.
If you only want to maintain the data between servers, you could install an additional disk, and then put the OS on that. Then just get the data from the other disk. Disks are cheap. Installing Win2k8 R2 doesn't take that long. Work out the costs against the cost of recovering your lost data!
Update Missed the bit about RAID when answering this initially. Would be interested to know if this affects things in two cases:
- Identical RAID controller in new machine - can it handle the RAIDed disks?
- Switch the RAID controller from the old machine into the new along with the disks. Does it work?
Worth knowing, as there are other things that can go wrong with a server than hard drive failure...