I had some trouble getting the z callibration correct, then I found this remark

Make sure you dont have a bed heightmap loaded. Send BED_MESH_CLEAR from the console to clear the heightmap. (https://github.com/bigtreetech/Eddy/blob/master/README.md#z-endstop)

and now it works. Maybe this could be added to the excellent documentation at https://github.com/vvuk/eddy-ng/wiki/Calibration