Here's the story, my son had his zephyr running with a 20gb hdd, that was till he got the rrod, the box was out of warranty and we knew nothing of the x clamp fix and with it being 4 days before xmas, he decided to go out and get a new elite with a 120gb hdd. So to transfer his content he got a transfer kit, tried to do it and now his console only recognises them when both are connected, one on the top and one by usb and then only gives him 16gb. When only one, the console cannot find any memory unit.
Is there any way to reset both hard drives so they both show their true volumes?

Did you use the official MS transfer Kit, with its software?
If not, which procedure did you use to transfer the files from the old 20GB?

Without my knowledge he used a cheepo kit of eBay, :-( and he put his new hard drive on the console and connected the old one to the kit.

I use the original Transfer Kit, when I got it, it was given free by MS for any XBOX you were owning, by just providing the Serial number to them. Anyway follow that Guide :

http://www.afterdawn.com/guides/archive/ac..._in_windows.cfm

or

http://forums.xbox-scene.com/index.php?showtopic=660096

Good luck!