Perhaps is dropping gently into the skill shot hole but hanging up on the switch thus the kicker can't reach it to kick it out. When my game was new - and I know of others - this switch was not adjusted down properly and the ball would just hang there not triggering the switch and not down into the slot far enough for the kicker firing to reach it. That could certainly happen on a slow right orbit shot too.

Also under the playfield you will find a BAG controller board and an RGB controller board. These have connectors that each represent a different string of LEDs. One of them may have backed out of its socket and need to be reseated. I'd check there first.

Or unplug the physical knocker.

4 LEDs on the apron are a leftover from the original non Bluetooth phone app connection. There were sensor stickers on the apron and glass that you put your smartphone down on to and the LEDs would flicker then light solidly when you were connected. Bluetooth now / no more stickers but the LEDs remain

You are correct yes.

See if there is any Mylar or residue on the magnet core that keeps the ball from rolling off of it smoothly