I'm not sure how it is today but this was my experience back in 2022 when I first registered for the use of eGates.

I had gotten a new passport in 2022. Flying SIN-KUL, I registered MDAC while in SIN (within the 3 day window of the departure flight). Landed in KUL and proceeded to the normal manned counters. While at the manned counter, I told the Officer I had registered for the egate. He acknowledged and said I would be able to use the eGate immediately on my return flight (which was in the next day or two since I was only there for a short weekend). On the day of the return flight, I used the eGate. Fast and efficient.

Since then all I had to do was register MDAC (within the 3 day window of the departure flight) and use the eGate when I land and return. Never encountered any problems so far. Very fast and efficient as I have said.

I'm assuming once I change a new passport, I would need to go through the manned counter again once to register the new passport number into their system.