Forget the Owners Manual. You need the Factory Service Manual: https://www.nicoclub.com/FSM/Pathfinder/2000_Pathfinder/
Specifically, get friendly with the Engine Control (EC) chapter: https://www.nicoclub.com/FSM/Pathfinder/2000_Pathfinder/ec.pdf
Codes can clear themselves depending on the "trip detection logic" and severity/type of code. Not that it helps determine the code, of course, but I'd start with EC-54 and get familiar with the system.
Then jump to EC-70. Have you tried putting the truck into diagnostic mode before? The 01+ trucks use a sequence of pedal presses, but the 96-00 will use a small screw-potentiometer on the ECM itself. On EC-72, that's the procedure to enter the diagnostic modes on the truck. Even if there is no stored code, it flashes a code to indicate there are no stored codes, and then shutting it off resets the ECM.
The first thing I would check is that the diagnostic screw is rotated fully counter-clockwise. If you attempt this, be careful as it can be fragile...use a small screwdriver with gentle turns...breaking it off isn't fun. Then, follow the procedure to trigger any codes, which get flashed on the MIL light in a long-short pattern. The FSM describes what to look for, and you can let it blink endlessly to ensure you've gotten all codes. An "0505" (5x long + 5x short) code means there are no codes stored.
Notably, I've had identical symptoms to what you've described, but on my 98 Frontier: truck ran fine, but every now and then the MIL would be on for a while, then go off randomly, but never return any codes. The reason I mentioned checking that the screw was fully counter-clockwise is because it needs to be in that position when not in diagnostic mode. Otherwise, I think it can leave the ECM in a diagnostic mode that monitors the O2 sensors. My situation is only unique in the sense that I had accidentally damaged the diagnostic screw and ended up soldering in a different style of potentiometer, and then eventually forgot which direction had become CC and CCW. As such, for years the ECM wasn't ready. I hadn't realized I had the rotation backwards until I needed to get it emissions tested and realized that none of the truck's emissions systems were ready despite years of driving. Ooops.