Sometimes the X and Y offset for the probe will mean the probe will probe past the edge of the bed if commanded to probe the edge of the bed. And so as we setup where we probe the bed we should take into considerations the commanded values of the X and Y offset for the Z probe. Moving your Y endstop changed the amount of MM on your Y axis and that is how I interpret what you are describing. You could also fix this issue by changing the probe positions or the X and Y offsets for the probe in relation to the nozzle or better both.