Windows 7: Hard drive problem on Windows 7

Hi all.

I recently got a virus which prompted me to format and reinstall OS...massive pain but had to do it. So I used my HP Microserver to backup by taking two drives out from my main pc (main pc data drive and main pc empty drive) and inserted them into the server. Since the server was full, I had to take out 2 hdds from the server for other backup purposes, we'll just call them server hdd1 and server hdd2. I did the backup but now here is a problem I have never faced.

Since I did not turn the computer off before replacing the drives, the server now sees it's server hdd1 and 2 drives which are now back in, as the main pc data and empty drives which I used in it earlier, and as a result, scandisk runs on every bootup and deletes EVERY FILE because it thinks that the drives are meant to be the pc drives, which do not correspond.

I have taken the drives out, rebooted, then inserted them so it detects them as fresh new drives but it appears that somewhere on the server hdd1 and 2 drives, there is an imprint left which tells the server that it's meant to be main pc data and main pc empty, and causes all these issues...

I won't dare run scandisk again as I have already lost a chunk of data, which is thankfully saved on an external. Please help!