It happens sometimes on my k8nf9. Im running F12k bios.
Here's what I do to resolve this issue:
1. Detach all IDE devices and sata (except primary hdd)
2. Connect HDD to any sata port
3. Go to the bios/integrated peripherals, disable IDE channels.
4. (Still in the bios/integrated peripherals) Mess with nv-serial ata 1 and 2 settings (make sure to note somewhere what the original settings are). Set it randomly a few times (reboot after each change) and check if bios detected your HDD, if not change something again. Try enabling raid etc, all combinations are allowed. You may switch ports hdd is connected to in the meantime.
5. Finally the board should recognize your HDD, set everything as it was before and connect other sata/ide devices.
I belive this method somehow resets a faulty controler or chipset, thus making it 'see' hdd/dvd again. This worked for me 3 or 4 times. My board 'forgets' my hdd more or less once a year. I dont know why, but I spent already too much time figuring it out.