HDD SMART capability is just the monitoring tool for reporting hard drive health. There's nothing really wrong with it being disabled, but if it's disabled, it obviously can't catch problems with a drive when it pops up.
You said you checked the BIOS and didn't see the drive listed anywhere, but did you see the working drive in there at all? If you didn't see either one, either the controller is dying, or your drives are set to auto detect, and the BIOS only looks for them on startup. Most modern boards will list them anyway when it's set to auto, but I've seen this happen in some cases.
Alternatively, get yourself to Windows, and open disk management (easiest way is to click start, then right click "computer" and choose "manage" then look for "Disk Management" on the left panel.)
Once in Disk Management, see if your drive is listed, and what drive letter it is using. Sometimes they'll swap drive letters out and you'll have a conflict, so the drive "stops working."
If the drive isn't listed, you can run a test to look for it. Grab Download Hiren
and burn it to CD or flash drive, and boot to it. Then go to DOS tools, then hard disk tools and look for GWSCAN (it was two menus deep in the older version, I'm not sure yet about the new one) and run the program. If GWSCAN can't find the drive, then you have a couple of options.
First, check the drive cable, make sure it's not loose, or replace it anyway just in case while you're checking it.
Secondly, the drive controller could have failed, or the drive itself. If it's the latter, swap the drive to another port on the motherboard if possible, and see if the system recognizes it. If not, you may have a bad drive and are just out of luck.