The grandfathering itself is an odd thing, since there is nothing in the copyright license that required Dish to stop selling superstations or to grandfather existing subscribers. It was simply a business decision that came out of the blue, with no real advance notice or warning (except for people who read the announcement on this site) and was implemented on an arbitrary date of Dish's choosing. (It is possible that the owners of the stations demanded these terms, as a condition for allowing continued delivery of their stations to in-market subscribers. The point is that it is still a condition that was privately negotiated, not one that was required by law.)
I think that Dish has been quietly trying to phase out the superstations ever since then, so they can reclaim that CONUS bandwidth for something else. They do not want to have a mass shut-off of superstations all at once, which would tick off a whole lot of customers and generate bad publicity. However, as existing customers voluntarily leave Dish, or at least voluntarily cancel their superstation subscriptions, it may eventually get to the point where so few people would be affected by their removal that Dish could easily drop them without blinking or giving it a second thought. So, I think that Dish hopes that disputes like this one drag on long enough that all of the existing grandfathered subscribers simply choose to drop their subscription and stop paying for the superstation.
If enough grandfathered subscribers start bugging Dish asking for refunds, while refusing to drop their subscription due to their grandfathered status, then that will force Dish to do the right thing, just to make the complaints go away. At that point, Dish will either bring back WPIX without retransmission consent (using the superstation copyright license) or Dish will start automatically crediting that charge back to subscribers' bills. If not enough people complain, then Dish will simply continue charging people for a service that is not being delivered, since nobody is trying hard enough to stop Dish from doing so.