If the lens sits on a shelve or what ever i might stiffen up and become unreliable or end up outside the parameters of the 'self' calibration area.
You can take the lens to Nikon Service to have them calibrate the lens, an also the camera in question,,,
All sorts of things can happen over time and one is the SWM focus motor, the surfaces degrade or get 'dirty' over time of course dependent on what environment it has been exposed to,,,
Here is Nikons how to:
https://nps.nikonimaging.com/technical_solutions/d500_tips/af/auto_af_fine-tuning/Nikon AF cameras always priorities to get the sharpest possible result and that is when the AF sensors see best peak sharpness.
Regardless of : Depth of Focus and Depth of Field.
In the software/firmware there are of course several rules build in for how the camera and lens software interpret the data and how the mechanical and electronics behave.
Also lenses have very different rendering in front of the focus plane and behind the focus plane so really tricky for the camera to guess where to compensate,,,
Using Live view is also an option, but often I am shocked at how narrow Depth of Focus is for the high mega pixel cameras!
Tripod setup must be quite stable, since the whole procedure involves touching buttons unless someone can figure out how to do it remotely
Good AF target and parallel to the sensor
Sensible distance from camera to target