When you boot the server you should be able to see the status of the drives. Replace the drive that is corrupted or not working, and you should see the Raid status change to BUILDING or REBUILDING or REPAIRING (or something similar). When you boot into Windows after this, you will probably not notice the rebuilding process.
If your onboard or 3rd part RAID utility doesn't show which hard drive is at fault, you can power down, remove a drive, power up, and see what your RAID utility shows for disk status. Do this until you find the faulty disk, then replace that disk.
Replacing the disk should initiate the rebuild, but you may have to manually start it yourself.