Once the 16U2 is in DFU mode, you will need to install the Atmel DFU drivers that came with the FLIP install.
After that, FLIP will find the device and you can program it.
Since you are programming it in DFU mode, you don't use the "COMBINED" version of the firmware. The "COMBINED" version is only used when you are using an external ISP programmer.
You want this file for DFU mode: ( Make sure you program the correct version for your board; Mega2560 or UNO )https://github.com/arduino/Arduino/blob/master/hardware/arduino/firmwares/atmegaxxu2/arduino-usbserial/Arduino-usbserial-atmega16u2-Mega2560-Rev3.hex