Peter, sorry about your annoying trouble. If the trouble emerged clearly after the service, the re-assembling failure (the sensor not sitting on the correct image plane) might be the culprit.
A properly calibrated lens/camera combo should work without problem even without the focus fine tune in the camera menu. My D750 and AF-S 50/1.8G combo (both bought new) had a slight de-focus issue which was addressed by the calibration at Nikon service. The AF-S 24/1.8G that I purchased as second-hand in a pristine condition showed also a slight focusing error which was addressed after serviced at Nikon.
According to the explanation by the service person at Nikon, AF-S motor should be stopped at the right position when it receives the "stop" command from the camera, but it can be misaligned for whatever reason, which causes the focus error and needs re-calibration.