kuba:
I think that if the board is responding to loopback test, the main chip seems to be working (correct assumption?)
Other way around. Your loopback test passing shows basic communications with the 16u2. The 16u2 "appears" to be functioning properly, so I suspect the bootloader on the Atmega2560 (main chip) somehow got zapped.
You are going to need one of the three things I mentioned before to get the bootloader back on.