With the right equipment, removing the Atmega2560 and soldeering a new one should be pretty straightforward. Once done, you need to make sure that the arduino bootloader is in place.

For this you need a programmer like the AVR Dragon. The connection typically would look like:

Connecting trigorilla ISP to AVR Dragon ISP

This is the wiring connection for the AVR Dragon to the Trigorilla ISP connector:

For flashing the bootloader, download and install avrdude:

• http://download.savannah.gnu.org/releases/avrdude/
• http://download.savannah.gnu.org/releases/avrdude/avrdude-6.3.tar.gz

• http://www.nongnu.org/avrdude/user-manual/avrdude_18.html#Unix

gunzip -c avrdude-6.3.tar.gz | tar xf -
cd avrdude-6.0
./configure
make
su root -c 'make install'

In /etc/udev/rules.d add (obviously as root user) the following file: 45-atmel.rules

# Atmel Corp. Dragon
ATTR{idVendor}=="03eb", ATTR{idProduct}=="2107", MODE="660", GROUP="dialout"

Then reload udev rules with:

sudo udevadm control --reload-rules && udevadm trigger

Steps and information below basically follow the description from here and here.

A bootloader can be found in the arduino directory from where you downloaded the arduino IDE itself. The location for Arduino-1.8.5 is:

Original bootloader:

../arduino-1.8.5/hardware/arduino/avr/bootloaders/stk500v2/Mega2560-prod-firmware-2011-06-29.hex

or the newer one that fixes the WDT and the !!! problems¹⁾:

arduino-1.8.5/hardware/arduino/avr/bootloaders/stk500v2/stk500boot_v2_mega2560.hex

avrdude -p m2560 -P usb -c dragon_isp -v

The original command would be:

avrdude -p m2560 -c dragon_isp -P usb -Ulock:w:0x3F:m -Uefuse:w:0xFD:m -Uhfuse:w:0xD8:m -Ulfuse:w:0xFF:m -e -v

But this command will cause avrdude to show an error at the verification step²⁾. To prevent this error, it is recommended to change this command into:

avrdude -p m2560 -c dragon_isp -P usb -Ulock:w:0xFF:m -Uefuse:w:0xFD:m -Uhfuse:w:0xD8:m -Ulfuse:w:0xFF:m -e -v

The reason is that only the lowest 3 bits from the lockbits are used. The other bits don't return any sensible value and causes avrdude to indicate an error. Ideally you would need to use a logical AND to filter for the lowest 3 bits.

avrdude -p m2560 -c dragon_isp -P usb -Uflash:w:stk500boot_v2_mega2560.hex:i -Ulock:w:0x0f:m -v

Similarly as in step 2, to prevent an error with the fuse setting at the verification step, change this command in:

avrdude -p m2560 -c dragon_isp -P usb -Uflash:w:stk500boot_v2_mega2560.hex:i -Ulock:w:0xcf:m -v

If you get an error like the following with avrdude:

...
Reading | ################################################## | 100% 0.05s
 
avrdude: verifying ...
avrdude: verification error, first mismatch at byte 0x0000
         0xcf != 0x0f
avrdude: verification error; content mismatch
...

You may have to change the fuse setting verification step³⁾. See above for the change.

• https://learn.sparkfun.com/tutorials/installing-an-arduino-bootloader/all