If you are unsure how to disconnect the Y axis stepper connection, that may be part of the problem, but the system doesn’t really know that it’s a gantry stepper or a rotary stepper and should not restrict you in the manner shown.
To perform the wiring swap, power off the laser cutter. Don’t change stepper connections with power to the controllers. Look in your wiring bay for a connector that is hanging free or stuffed in a corner or raceway. It is the cable that runs to the bulkhead to connect to your rotary.
Find your y-axis stepper controller. It might have a marking that indicates it’s the y-axis, it might not. Match the connector hanging loose to the one on the controller, gently pull the existing one out and insert the previously-loose connector in its place.
When you power up the laser, the gantry should not move, but the rotary stepper should spin. It will be seeking the limit sensor. You can expedite the process by bringing a metal object near the y-axis sensor a couple of times, or you can wait until the seek times out.
I don’t think this aspect is related to the lack of selecting the Y axis in the software, but I could be wrong. I’ve been wrong before.