534 - MachXO: Why can't I scan or program the MachXO device on the MachXO Mini board after I programmed my pattern into the device?
The MachXO JTAG pins on the MACHXO Mini board share the same traces with some generic IOs of the MachXO device (as shown on page 4 and page 2 of the schematic). If the new design patterns have signals driving out of these pins, they could potentially corrupt the JTAG signals and cause the device failed to be scanned.
The generic IOs that share the traces with the JTAG pins are pins 28, 30, 31 of the MachXO device on the board. You should neither assign output signals to these pin locations, nor leave the software to automatically assign pins to these locations. It is suggested to lift up these 3 pins if the board fails to scan after a new pattern is programmed into the device, and after the proper programming steps in the Users Guide are followed.