The Brainlink firmware is open source, and you are encouraged to modify it. Brainlink's release firmware runs on an Atmel Xmega controller, and is written in C and compiled with the freely available AVR-GCC. Brainlink includes a bootloader that reprograms the main program over its Bluetooth connection - you do not need any special programming equipment to reprogram the firmware.
Alex Pruss has continued developing the Brainlink firmware after we discontinued the product. We suggest checking out his version as it fixes a number of bugs and adds a few new features. If you wish to update your firmware to Alex's version, we recommend using his firmware updating Android App.
Visit the Customizing Firmware tutorial for a detailed description of how and why you'd modify the firmware.