Thanks for taking the time to reply but your reply was not very helpfull :/
You should be able to bypass the USB chip and program via the ICSP header. You need a programmer. You can buy something like the USBtinyISP for around $20, or just use another Arduino as the programmer.
Or 3.5 usd http://www.ebay.com/itm/USBasp-USBISP-3-3V-5V-AVR-Programmer-USB-ATMEGA8-L-/140763404046?pt=LH_DefaultDomain_0&hash=item20c627170e