well, yeh. This is a very important observation.
It is likely that the bootable harddrive is the one not showing in the cmos.
However, there are times that motherboards do not recognize a harddrive and
requires
a user input, like from you. As a user input you need to check if your cmos
clock is accurate, see
if the disks/devices are recognized. Most motherboards provide an f key to
help the average user
automatically set the cmos to optimized settings or basic defaults.
Somewhere in the cmos, the size of the harddrive should appear and it is
likely to be your slave your drive.
The primary drive is likely to be the one not showing and therefore that
line in the cmos settings are blanked out.
Most if not all motherboards have a key to press to auto search the
harddrives - maybe it could be the f3 key. But check around. The parent
website to the unseen harddrive can also provide the cmos settings that you
can enter manually.
If the hard drive still doesn't show, then maybe the cabling to the physical
drive wiggled loose or something, as no power to the hd would make it appear
not connected to the motherboard and unseen by the cmos.
If you feel you have no choice but to load windows onto the harddrive that
is recognized, then you will have to configure it as the primary drive. And
then your windows cd will begin to work again. If you have a smart drive,
then you can simply redesignate the slave harddrive as the primary/master.
If not then you may have to physically switch the cabling and connect it as
the master instead of the slave. There may be also be a little connector on
the back of the hd that designates it as a slave or master of slave/master
setting. You may want to switch the other harddrive as well.
Its possible that you can get windows back online then you may regain access
to your system. At least temporarily until you get a new hd if needed......