Well... you're certainly correct. That second drive is gone.
Is that second drive with E on it a SATA, IDE or SCSI drive? Internal I assume, although you didn't specify. Or is it an external USB drive? Or something else?
Is it visible in the BIOS? If you get into the BIOS at machine boot time, does it show up in the list of hard drives? Or is it gone even from the BIOS's perspective?
Have you tried just pulling the power and data cables from it, and then re-seating them?
If it's a SATA drive, have you tried pulling the SATA connector to the motherboard and trying it in a different SATA connector on the board?