I’m not sure what would have caused the issue you described, but here are a few things I would recommend checking.
- Ensure the BrickPi3 boards are stacked correctly, with proper header pin alignment and adequate depth.
- Power each BrickPi3 with it’s own battery pack, with both power switches in the ‘ON’ position.
- Make sure the RPi header pins are configured for the BrickPi3: enable SPI, and ensure the SPI pins are configured for SPI communication rather than as GPIOs.
If the issue re-surfaces, try the above, and report back if it’s still not working.