loosen all 8 bolts holding the X rail to the Y rails.
reboot the controller
move the Y rails to the front with the joypad as far as you can, so that both y gantrys hit the y feet and come to a resting point up against the feet (you may hear the motors grind during this process, this is normal and will not damage the machine).
Once both Y’s are correct, tighten down the 8 X rail bolts.
Reboot and rehome
If you are still experiencing issues, you may have a greater issue with a Y axis.
If so, follow this FAQ:
Also, make sure your machine wasn’t set up as a parallelogram.