It sounds like Y is moving OK but in the wrong direction. I would swap Y- left and Y right at the control board and try to home again. Start with the axes in mid travel so you can abort if they don’t head in the correct direction or sound bad. If this doesn’t straighten it out then a detailed review of the Y axis cabling with the support team is in order.
I had a situation where this issue started out of nowhere. I was instructed to disconnect the X & Y wires reconnect them and verify the Homing Switches were operating properly.
Doing this took care of my issue.
I have never gotten use to that sound. It is really irritating.