Asus bioses suck. Yep, I said it.
To answer your actual question: the only reason a drive won't show up is if it's dead or the mobo can't detect it (which usually means the drive's board is bad). But you would get warnings on boot if the board detects a failing drive thanks to S.M.A.R.T. (I'd suggest hwmon but you can't boot so it's moot).
Go into bios and make sure the drive that you want to boot is set as the boot drive.
Since you can't see the drive, try taking out all the other drives and going into bios. This can also be an issue w/ raid vs SATA vs PATA/IDE and sometimes EFI/UEFI can cause issues with actually booting to windows, but it sounds lower level than that.
With Asus, the actual place to set the boot drive is often in some obscure, un-intuitive place. It usually has a boot order but only one drive can be selected per slot and typically the boot select screen is not the drives select screen; however, it might still be set but not be picking up the right order (I had an asus board that would forget from time-to-time which one was the right drive to boot from and re-order my disks so it would constantly fail despite saving it to a profile; needless to say I have a lot of animosity with asus boards). If you poke around there should be a disk or storage option that shows all the disks attached and a completely different and illogical screen to actually set the boot drives.
Anyway, I wouldn't go mucking about with BCD if it booted at one point. My setup was/is boot from some old C: drive but start up the SSD I had added and moved windows to. So yes, BCD is useful in those types of situations if it is not booting from the correct drive or if the MBR is on a different disk than the windows installation. If you find the correct drive is setup in bios properly, then by all means muck around w/ BCDedit....but if it's not even letting you set the right boot disk, then it's probably not a windows/MBR issue.
Sometimes reordering the phsyical sata connection helps too, but only if one of your sata ports is going bad (and it just happens to be that one).