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When they changed the actress playing Oracle mid-sequels in Matrix, they made up an in-universe explanation for it.
Was there an in-universe explanation for a change of actress playing Eviel in the Mummy sequel #3 (The Mummy: Tomb of the Dragon Emperor), when Rachel Weisz was replaced with Maria Bello?
In terms of canon, all we have to go on is the content of the film itself. No in-universe reason was given in it for the very drastic changes in Evie's appearance and persona.
In Matrix Revolutions (which you refer to), the Oracle was a program and that was something that was easily exploited to explain the change in her appearance.
However, Evie is a flesh-and-blood human being. True, there are various supernatural forces at work in the Mummy trilogy, but no appeal was made to those as a means of explaining Evie's changes.
