Don't think so. The CMOS will boot from whichever HDD it thinks is primary.
I'm not sure quite what BRL is trying to do - he's made the former Drive D bootable; does he want to keep it like that (so make it Drive C), or make the new one the bootable and C? It's all down to the jumpers, but it's hard to format a new drive as bootable and C if there's already a bootable drive there - you risk formatting your existing drive and losing everything off it.
I wonder what else was on the now-dead drive C? Apart fron the operating system (no problem to replace that), I mean.