Vulture reveals that ScarJo had actually stepped in to replace Samantha Morton. But this isn't the result of some on-set dust up or fractious split between director and star. Instead, it was a choice made after filming had (initially) wrapped. "Samantha was with us on set and was amazing. It was only in post-production, when we started editing, that we realized that what the character/movie needed was different from what Samantha and I had created together. So we recast and since then Scarlett has taken over that role," Jonze explained in statement.
That being said, don't expect ScarJo to be seen on screen -- she's taking Morton's voice role as the OS that Joaquin Phoenix's character falls for. This isn't the first time this has happened and Jonze has a bit of a reputation for "finding" the movie in the editing room. The same thing happened on "Where The Wild Things Are." Michelle Williams was originally hired to play the voice of the monster KW who befriends Max. However, in the editing room, Jonze found her voice characterization of the character didn't quite work so her voice work was ultimately replaced with that of Lauren Ambrose's (Williams and Jonze dated, so there probably weren't any hurt feelings there).
The movie was the first collaboration between the director and actress (though Morton starred in "Synecdoche, New York" which Jonze produced) and he takes full responsibility for her exit, chalking it up to his "not-quite-painless-for-everyone-involved 'process' " and hopes that he gets to work with Morton again.
So, a bit of bummer for fans of Morton (as we are) but it still leaves us as curious as ever for the film, a oddball romantic comedy about a man and his operating system (really). Additionally, if you're at the L.A. Film Festival this weekend, the first footage will be screened during a panel discussion about Jonze's work, with the filmmaker participating in a Q&A.