Reprogram Atmega 16u2 on Arduino Mega with Arduino IDE?
Yes, you can recover the firmware in 16u2 only with Arduino IDE installed. In subfolder hardware/arduino/avr/firmwares/atmegaxxu2/ of the IDE installation folder is the hex file of the firmware Arduino-COMBINED-dfu-usbserial-atmega16u2-Mega2560-Rev3.hex. The README.txt file in that folder has sample command line to upload the firmware with avrdude.