I’m having an issue very similar to this one here, although I don’t think I can easily downgrade the BIOS: http://community.wdc.com/t5/Desktop/WD1001FALS-Disappears-randomly-on-Windows-7-x64/m-p/136306
I bought a new computer and I have a 120GB SSD as my primary drive working fine, and I have a WDC WD2002FAEX-007BA0 2TB secondary drive (SATA 6GB/s connection) reporting no problems. SMART diagnostics show it working fine.
Randomly after an indeterminate period of time it just disappears from Windows completely. Applications loaded from it will stop working (usually - Firefox sometimes will let me continue using it, probably because the main app is loaded into memory), the drive disappears from my computer and disk management, and is gone from resource monitor. If I reboot, it shows back up fine as if nothing happened. When I was setting up VMWare, I could force the drive to disappear by trying to save the new imported image to the drive. I’ve since imported the image to my SSD instead, but I just mention this as I found it odd that I could actually force the drive to disappear by taking a specific action like this.
I’ve updated my BIOS and disabled ACPI drive power down, without change. I am not sure if BIOS is set to IDE or AHCI, but where users have changed this setting in my limited research, it hasn’t made a difference regarding the issue at hand. Googling the general issue (drive disappearing in windows 7) shows this seems to be somewhat common, especially with larger drives, and not specific to WD drives or my specific drive model. Still, I have not found an exact solution for the problem yet.
I’m going to double check the cables today, although the fact that it loads up and runs fine for a while would indicate that the cables are most likely connected fine.
Any other suggestions appreciated. Just please keep in my mind - my A+ certification is expired by about 2 years so while I’m comfortable working with computer software and hardware, my knowledge of the current technology is minimal, and detailed explanations are appreciated. 
