ICSP (In Circuit System Programmer) for those (2)3x2 headers which are the SPI connections to the 8u2/16u2 and your Atmega2560. USB Tiny, USBasp, AVRISP, etc connect to these headers. You also can use another Arduino as a programmer. I have not tried the Atmel FLIP or the dfu-programmer, but here is the link:
I just do not know if this will work if the DFU is really messed up. Using the ICSP is a lot cleaner, to me.