Reformatting is basically erasing everything on your hard drive and reinstalling your operating system (XP, Vista blah blah)
if your gonna do this I suggest you get backups for your files so you don't have to go around and look for em all again.
Reformatting Your Computer Using Windows XP - ITS Help Desk - The University of Iowa
heres a nice site for XP version, dunno about the others though.
Anyways, I have trouble with the patcher too, can't even finish x2.exe without it 'looping', most likely i got some trouble connecting to their patching server, gonna try again tommorow