It sounds like you are following the practice instructions perfectly. I would continue to note and observe the arising and passing of phenomenon (in this case, pain). The more you meditate, the more you will see that no experience exists outside of the conscious knowing of an object (which includes pain). So when you no longer can observe pain, that pain is gone, completely, until conditions arise for the pain to return (i.e a physical stimulus and sensation of pain and the mind knowing it). So to answer your question, I do not think that the mind is burying or ignoring the pain, the conditions required for the pain to arise simply don't exist anymore in that moment of disappearance. You can compare this with the rising and falling of the abdomen. When you note "rising", the conditions are present for knowing of the rising of the abdomen. When your finish noting "rising", those conditions have ceased and the rising is gone, completely, just like the sensations of pain.
You should also take the opportunity to note the mind state of "wondering" or "curious" or "analyzing" or something similar if you find yourself wondering if the pain is still present.