It appears that the preprocessor symbol HEXFILE_Arduino_COMBINED_dfu_usbserial_atmega16u2_Mega_Rev3_hex_Full was at some point removed in favor of HEXFILE_Arduino_COMBINED_dfu_usbserial_atmega16u2_Mega2560_Rev3_hex_Full. Not all references to this older preproc symbol were updated, resulting in an inability to flash the original bootloader onto a Mega 2560 Rev3.
It appears that the preprocessor symbol
HEXFILE_Arduino_COMBINED_dfu_usbserial_atmega16u2_Mega_Rev3_hex_Full
was at some point removed in favor ofHEXFILE_Arduino_COMBINED_dfu_usbserial_atmega16u2_Mega2560_Rev3_hex_Full
. Not all references to this older preproc symbol were updated, resulting in an inability to flash the original bootloader onto a Mega 2560 Rev3.