Hmm this dissapearing hard drive problem popped up again for me last night and this morning.
I noticed that it was always happening to any hard drive connected to two particular ports on my P45 motherboard.
I noticed both of these ports had the same SATA type cable, the green UV one that came with my DFI motherboard, while the perfectly fine ports had generic SATA cables.
I swapped the green cables out, low and behold the ports work fine.
So jarthel, maybe try swapping SATA cables around to see if your dissapearing drives stop dissapearing.