Changes in grosses depend heavily on the popularity of the show. Fun Home has been doing good business right along. As far as how actors/actresses are paid, it has more to do with how much they contribute to the show than how well the show is doing. I'm sure Chita Rivera was paid more in The Visit, which did not do well at the box office, than Sidney Lucas was for Fun Home, which was a hit. Rivera is a big name and Lucas wasn't at the time her salary was originally decided (and certainly not in the same league as Rivera now).
BROADWAY: The Cripple of Inishmaan, This is Our Youth, If/Then, Hedwig and the Angry Inch (x3), Cabaret (x2), The Real Thing, A Gentleman's Guide to Love and Murder, Chicago, Les Miserables (x2) Disgraced, Finding Neverland, On the Twentieth Century, Wolf Hall Part I, On the Town, Fun Home; TOURING: Jekyll and Hyde, The Book of Mormon; LOCAL: The Twilight Zone, Anne Boleyn, Death and the Maiden, The Lying Kind, Chorus Line, Stupid F**king Bird