A $25 OBDII reader will clear pending codes, so that should take care of it.
If the ECU records a log of when it was accessed and cleared it's news to me.
That said, you shouldn't have anything screwed up with shifter actuation/gear selection just from having it Neutral... I'd clear the code, put the OEM shift knob back on, and see what happens. If it starts doing it again, take it to Nissan to investigate.
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Enjoy it. Destroy it.
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