Was the ECU originally a 4l60e and if so how did you change the wiring and segment swap for the 4l80e, for mine it was both segment and a re-wiring job
If the ecu is originally 4l80e I would double check the pinouts are what you think they are and that somebody didnt do some weird 4l60->4l80e stuff to the harness
Its weird that it worked and then doesn't suddenly. Could be a wire is crushed in the harness maybe its shorting where you can't see it so it seems like the pcm is doing things but its really just a short?
Maybe disconnect the harness from the PCM and check the wiring for obvious continuity or shorts between the wires and to ground/12 even though its disconnected