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Your RESET circuit is wrong. You have no pullup resistor on the RESET pin of the ATMega3560. You have an extraneous pulldown resistor on the D7 pin of the 16U2. That means your 16U2 will not be able to trigger a reset of the ATMega2560 to run the bootloader. Remove the pulldown on D7 of the 16U2 and add a 10kΩ pullup to the RESET pin of the ATMega2560. ...


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Do I need to remove the Microcontroller Chip from the DIP socket before burning firmware? No, just connect RESET to GND to stop the MCU from running. Does it going to affect Arduino Bootloader? No.


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