Попробовал, вот:
avrdude.EXE: Device signature = 0xffffff
avrdude.EXE: Yikes! Invalid device signature.
avrdude.EXE: Expected signature for ATMEGA2560 is 1E 98 01
avrdude.EXE: erasing chip
ft245r: bitclk 230400 -> ft baud 115200
avrdude.EXE: ft245r_program_enable: failed
avrdude.EXE: reading input file "ATmegaBOOT_168_mega2560.hex"
avrdude.EXE: input file ATmegaBOOT_168_mega2560.hex auto detected as Intel Hex
avrdude.EXE: writing flash (256444 bytes):

Writing | ################################################## | 100% 97.30s



avrdude.EXE: 256444 bytes of flash written
avrdude.EXE: verifying flash memory against ATmegaBOOT_168_mega2560.hex:
avrdude.EXE: load data flash data from input file ATmegaBOOT_168_mega2560.hex:
avrdude.EXE: input file ATmegaBOOT_168_mega2560.hex auto detected as Intel Hex
avrdude.EXE: input file ATmegaBOOT_168_mega2560.hex contains 256444 bytes
avrdude.EXE: reading on-chip flash data:

Reading | ################################################## | 100% 44.81s



avrdude.EXE: verifying ...
avrdude.EXE: verification error, first mismatch at byte 0x3e000
0x0d != 0xff
avrdude.EXE: verification error; content mismatch

avrdude.EXE: safemode: Fuses OK

avrdude.EXE done. Thank you.
Судя по всему проверка не прошла