By upper limit I am writing about a shutter speed that is high enough that its capture period is shortest that still allows the VR servo follow a full vibration cycle. Above the 1/2 the sampling frequency is just as likely to capture a the image before or after the servo driven optical element can detect the error sample that is used to determine which direction to shift the element. In information theory, the highest rate of change that can describe a signal accurately is 2 full samples With a sample rate of 1000 times a second, the highest frequency that can be described would be 500hz. Vibrations faster than that or shutter speeds shorter than that produce ambiguous data, That is why the recommended shortest shutter speed that VR is predictable is 1/500 sec. As a result of this useful limit the servo designers put in a low pass filter to not respond to vibrations higher than 500 hz. The same principle is used to accurately handling 1/2 the sample rate in digital audio. CDs had a sampling rate of 44.khz so any frequencies higher than 1/2 that needs to be filtered out to prevent alias distortion so the highest frequency single component ia 22.050khz.
Yes, "it" was the VR system. What is being tracked is the vibration, if there is a predictable period detected by the servo it can predict quite accurately where the optical element needs to be in a given number of samples. The more data samples the higher the prediction quality is possible, hence the comment about 1/250 shutter speed will allow twice the number of data samples than 1/500.
To focus and recompose, you need to stop the AF from activating again after desired focal plane is achieved. The requires pressing the AE-L /AF-L button to lock focus. The best way for most of us is programming that button to be AF-On, and another button for the exposure lock. I use the AE/AF-L button for AF-on and the Fn button for exposure lock. I prefer that to the dedicated button of the pro bodies that have two thumb buttons next to each other as on the pro bodies Stan St Petersburg Russia