Shoot… the gcode execution was flawless, but the collet-bolt was tightened so much that when I unscrewed, the gantry was pushed a little… I guess I should be a little more gentle when thightening. It makes sense that the ends stops are not able to recreate the zero in a fashion that eliminates any traces, layers or shifts… at least my endstops, that are rollers. It’s hard to imagine that they can hit on a tenth of a millimetre.
Edit: The CNCjs interface told me to press resume to continue, but I also had to toggle the LCD switch.
Edit again: regarding the pause/LCD issue: CNCjs & M0 Wait for User