If the disks are in stripe mode:
Forget swapping one disk at a time.
(Not that I see a sane reason for anyone to use stripe in a server, but for completeness sake.)
Assuming your disks are a mirror. (If you do not know what that is, read this post on this site It explains what the RAID levels are).
If it is hardware RAID:
both identical hardware, but double check if the RAID cards are of the same manufacturer. Most (all?) seem to put their RAID configuration on the drive. Which means you can swap one drive and insert another empty drive. Then rebuild/clone.
If they are not the same then it becomes a gamble. Same brand but never model will probably be fine. A different brand might be a challenge.
If it is fake software RAID
(IRSSI, Intel fake RAID etc.), then make sure the motherboards are the same. Again, you wrote that
both identical hardware, but check. Different motherboards, chipsets and possibly BIOS/UEFI versions matter here.
I do not have much experience here, but general advise seems to stay far away from this. Either use plain software RAID, or use hardware RAID. I realise that this conflicts with your need to make a clone of the windows server, but if you are setting up a second server then now is a good idea to do it properly.
If it is normal software raid:
(LVM?) I never used this under windows. Best follow @MikeB's advise.
If the disks are in neither stripe nor mirror:
You will either need to use some form of backup- and restore-software. Or recreate one disk at a time by pulling a live drive out of the original server, and replacing it with a clean drive. Then do that for all bar one drive.
Note that I would not feel comfortable doing that. Esp. if the original server uses large disks in RAID5.
Regardless of what you do:
- Make sure you have an up to date backup.
- If I could repeat item 1 in blink tag, it would go here. Really.
- Actually test that backup.
- If you clone the server and it is not a domain controller read up on possible problems with unique identifiers in windows domain. (Which will not be unique if you clone a drive).