It is the main part of a major shakeup on the series, which also includes the departure of fellow original cast member Tamala Jones. Fillion has been in negotiations to return to Castle, which I hear is eyeing a shortened, likely 13-episode.
TVLine has learned that in the 19th episode of Season 8, Silverman plays Alan Masters, the miraculous survivor of an attempted murder who subsequently helps Castle and Beckett solve the case.