Forgive the silly question, but you unplugged the drive, rebooted...Then shut it down and plugged the drive back in? Or did you plug it back in while hot?
Bpierini, actually what I did, right or wrong, was everything was working and Vista x64 was booted. Then I unplugged the sata cable to one drive. Shutdown then plugged in the sata cable back in and rebooted.
What is not safe to do? Unplug power while running? Plug sata in while running, plug both in while running? Is sata hot pluggable?
SATA is not hot pluggable (sp?) I'd try shutting the wsystem down, plug the SATA drive cables back to original. On boot, go into BIOS and make sure both drives are recognized. You don't say what OS you're using, I'm guessing this is software RAID1? If the system still doesn't recognize the mirror, give it a little while, then go back into the software and see if it's sill configured as you expect. If not you may have to reconfigure.