games disappeared off drive...

Ok so a while ago I bought a hard modded Xbox with a bunch of games on the drive. The drive was partitioned, with several games on each partition. I lent it to a friend recently, and all I really showed him how to do is get into the game list. He claims what happened is when he loaded Forza, the game crashed, and most of the game list disappeared. I checked the drive the best I know how and it seems to have a ton of free space available now and most of the partitions are gone as well. Only 2 games stayed, both on the same partition. I accept the fact that the games are gone, but what I want to know is what happened? More importantly, I would like to know if I were to format everything and start fresh what steps would be involved? I am most interested in setting up the console for emulation of older console games such as N64 and older.

[EDIT:] I should mention that to my knowledge my console had an x3 chip build 3039 and had EvoX 2.7 installed as a dashboard.

Basically, I want to take this mishap as an opportunity to set my unit up properly, something I should have done a long time ago.

Where do I start and what steps do I take from there?

[EDIT:] Still awaiting a response on this...