Hey CJ,
it is unlikely that the software upgrade has an effect on this, however 1.0.9 is stable, I use it too.
Did you check all contacts of the connectors? Sometimes their strands went out of the crimp as shown here. Sometimes they have simply a bad connection due to wear or corrosion of the tin plating. In this case, a little amount of KONTAKT 60 and then KONTAKT 61 can help.
What I would do is to disconnect the motor cable of the corresponding axis, and with a multimeter set to resistance (ohms), measure for conductivity from end-to-end, on all four wires of the cable. I would do this with both portions of the cable, first measure the cable you can detach easily, the one from controller to axis, and then the one from axis plastic end cap to stepper. This however is not easy as on Y motors, there is no connector at the stepper end. There is one inside the chrome-plated tube though. But before disassembling it like described here: How to access the inner tube motor wire, you could measure the coils of the stepper from the outside (lowest ohm setting on multimeter), by looking at the Onefinity Wiring Diagram. There are four cables that go to two coils, so two cables per coil (see also How are bipolar steppers wired?). Note the cable cross on the second portion of cable.
Then I would attach the external cable to the axis again and repeat measuring the coils at the end of the cable (the end that would go into controller).
There is a thread somewhere in this forum where someone posted how much ohms a coil has, it is in any case a very low value (<100 Ohms).
However if you are already sure that the Y2 motor looses power, and you are sure the contacts of the connector are okay or not, as described here, I would swap over the Y cables and check if the motor works correctly then and the other Y motor makes the problem then. I know they’re of different length, hopefully you can put the controller somewhere to allow this. If that is not possible, I would simply order a replacement cable.