It doesn't sound like it was anything serious, Eponine. I dug up some articles surrounding her dismissal or departure, however you want to label it.
Here's an article from TheaterMania comparing Brad Oscar assuming the role in The Producers after Henry Goodman got canned to Sutton Foster winning the Millie role in the same way.
"Between your show and Thoroughly Modern Millie, this is really the Year of the Understudy. Erin Dilly missed some performances of Millie in La Jolla, Sutton Foster went on, the powers that be decided that they liked her better in the part...and it was so long, Dillie."
http://www.theatermania.com/content/news.cfm/story/2197 Playbill also wrote an article on it.
"Many a journalist will miss the Erin Dilly-Thoroughly Modern Millie rhyme. The young actress, who made a splash in Babes in Arms and Martin Guerre, was set to perform the title role in the La Jolla Playhouse production, but several production meetings later, she and the creative team determined that Dilly would not be able to continue with the show."
http://www.playbill.com/news/article/55640.html