I am inclined to think that it would be very difficult for you to run afoul of the second home rider, even though, technically, this situation would fall outside of the "suitable for year-round occupancy," and perhaps other provisions as well. In reality, the holder of that Note is trying to make sure this is not an investment property, and it would appear that you have a strong case that it is not. Ultimately, all of us on this board would defer to an attorney, but this is my take on the real world situation.
Finally, RPM offers a program called "Family Opportunity." This allows an owner to classify a property as a second home instead of a rental if the occupant will be an elderly parent or a child with medical needs who otherwise would not be able to afford housing on his/her own. So, in a sense, you may already be using your second home in the intent of this program.
If you have any questions, just get in touch.