Bizarre Boot Failure Insert System Disk

I'm working on a machine that seems to somehow only run DOS. Windows is not detected on the machine. We bought this from a company in order to do simple testing on some of our products. Upon powering up one day (No change to HD cables or power cables) I got the "Disk boot failure, enter system disk" message. The only means to have a disk on this machine is the USB port, which is empty.

The company that we bought the machine from provided us with a backup flash drive to boot from in case this computer went on the fritz like it has now. I'm able to start up the program from the flash drive, but obviously once removed it will crash.

I'm trying to find a way to wipe the drive, and then reinstall this program on the drive. The drive's contents are still readable so I don't know if the drive is actually fried or not. I'm not sure how I'd install dos again if I flashed the C: drive either.

Any thoughts?
 
I'm noticing now that the drive that is being recognized as C: is actually the back up flash drive. So I'm actually not sure I'm able to read anything off the hard disk. Is there a way to check if the hard disk is done? I'm also noticing at the initial screen it's listing the primary drive and slave drives as "none"
 
The flash drive is C because Windows doesn't recognize the actual boot drive. Remove the flash drive and see what happens. Tell us, what you notice
 
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