Maybe someone with better understanding than I can answer this for me. Considering that the score of the show is done by various pop artists contributing a song, could the royalties on that be part of why the show is struggling financially?
Also, Nederlander has pretty much ditched the whole construction project that would take five years. Ever since An American in Paris (Nederlander said that when that show closes the construction would begin), it kept getting pushed back and pushed back. That was why it was able to play host to Sunset and now SpongeBob. In fact, Disney wanted The Palace for Frozen since that theatre is a set designers dream. But, at the time, Nederlander was waffling over the project and couldn't get its act together. Thereby, leaving Disney to say thanks, but no thanks and go elsewhere, hence them being in The St. James (and, keep in mind, every other Disney show on Broadway that hasn't been in the New Amsterdam has been in a Nederlander house.)