motherboard wont detect my ssd?

[pyr0_m4n]

Ok, so this has me stumped. I have a 180gb ssd i use as my primary drive. I also have a 500gb hdd i use for video editing. Yesterday, my 500gb stopped detecting in BIOS. I opened the case today, removed it, then turned the computer on. I couldn't boot my OS anymore (which is on the ssd). I was about to wipe the drive when I thought to put the 500gb (which wasn't being detected by the motherboard BIOS anymore) back into the computer. Not only did it boot up like normal, but now it's being detected again and everything seems to be intact data-wise. I'm at a complete loss. Two major questions here.
1. Was this a mobo problem?
2. How does taking out a drive affect my primary (even though the OS had nothing to do with the 500gb)

 

[smorizio]

Run hdTune on your hard drive see if there any smart warnings. Could been the drive was slow to spin up and hung. For the booting issues if the hard drive was connected when you installed windows the system restore partion may be on the hard drive. If it is you have to use windows boot tools to make the Ssd bootable.

 

[ur6beersaway]

In bios are you using ACHI or IDE sata setting?