Sort of...I expect it's the typical sort of incestuous arrangement like 'Walking Dead' has with AMC: an accounting drill to screw over someone outside the A&E or AMC corporate team, by means of the production company not making much on paper, while the distributing network rakes in all the real revenue...with the production company being just in reality a hollow puppet for the distributing company. The number one way to get screwed in media is to make a deal that involves getting a percentage of net profit, when you're going to be getting paid by the person who gets to calculate that net profit.
A&E does in fact own the rights to all the seasons including this, that does not mean they have a right to content control. They either air an episode as is or don't. Remember, reality shows are way different than dramas like Walking Dead not only the obvious, the on screen people on realities are contracted through the production company, where as actors are under contract to both. Actors are paid more because of the actor unions than realities. The difference is, one, Robertsons had a small business that turned successful not just because of A&E, they also had another show before that and a series of successful home videos still adding on to this very day.
The best way to protest this removal of Phil is to return all Duck Dynasty gear that was bought in stores and purchase the Robertson gear directly through their Duck Commander website. The ones you see at a store A&E get a major percentage of, where as Duck Commander goes straight to Robertsons 100%.