1778 - MachXO2: Can I really use the PROGRAMN pin for user i/o without disrupting the ability to program a blank device in-system?
At issue here is that for an erased device PROGRAMN is active by default. There could be conflict if the user circuit has this pin held low during the MachXO2 power-up sequence. Fortunately, the JTAG port will override the PROGRAMN pin in this case.
The user design (bitstream) will load properly. With SDM_PORT=disable PROGRAMN, INIT and DONE are then available for GPIO.