ok you are doing a Referenz on index pulse.
means the ref Limit Switch is very secondary.
reference on index pulse means go t reference Switch reverse direction and look for the next Zero pulse of Encoder.
it has done this before and it's an easy fix, just flip the belt round one step on the pulley and re-ref = all ok.
this teels me that you have a seperate Encoder for Feedback Loop, witch is belt driven.
ok if you shift this belt for one step, it is "normal" that yor home pos shifts as well (index pulse !!)
Thomas