You can reprogram the boards without disconnecting them by using a 6-pin ICSP cable. One programmer that works well for me if the adafruit USBTinyISP (adafruit.com/index.php?main_ … ucts_id=46). You do have to pull off the LED matrix to get access to the header, but that’s often easier than disconnecting a long series of boards. The avrdude software can burn the .bin file that the Arduino environment produces, just make sure to not overwrite the bootloader.