Hi,
what motion controller are you using?
I don't have a gantry so I could be out t lunch here...I believe the motion controller has to temporarily break the master/slave connection between the two
motors and home them individually. It requires active participation of the motion controller to do it.
I know, and have read a good part of a thread called Auto Squaring on the Warp9 forum, of course it relates to their USS and ESS products.
Craig