Daphne Rubin-Vega was fired from the first Les Miserables revival. She took a leave of absence to appear in Jack Goes Boating at the Public, always intending to return, but the producers bought her out of her contract in the interim and kept Lea Salonga on as Fantine. Later on in the same production, Mandy Bruno and Ben Davis -- the first replacements for Eponine and Javert -- were also fired very shortly after taking over their roles.
Other instances I don't remember seeing mentioned here yet:
--Barbara Barrie as Yente in the 2004 revival of FIDDLER (replaced by Nancy Opel in previews)
--Carolyn Migrini as Sarah Brown in the 1992 GUYS AND DOLLS (replaced by Josie de Guzman in previews)
--Dorothy Loudon as Carlotta in DINNER AT EIGHT (replaced after one performance by Marian Seldes)
--Caryn Lyn Manuel in THE TIMES THEY ARE A-CHANGIN' (replaced in previews by Lisa Brescia)
--Lee Remick in as Martha Livingstone in AGNES OF GOD (replaced during the pre-Broadway run by Liz Ashley)
--Garn Stephens as Petra in the original A LITTLE NIGHT MUSIC (replaced in Boston by D. Jamin Bartlett after a handful of performances, mostly because Stephens couldn't handle the role vocally)
--Melora Walters in Stephen Belber's play MATCH (replaced in rehearsals by Jane Adams)
--Santino Fontana in A VIEW FROM THE BRIDGE (replaced by Morgan Specter after being injured in previews -- of course, some claim that he was blocked from returning from the production, but I don't have any idea if that's true or not)