So, presumably, these stories were rewritten to include her again. But what I'm really wondering: if Clara was supposed to be gone, who was supposed to be in her place? Was this going to be a Companionless season? Was Missy supposed to have more of a full time role? Was some random new person supposed to have been introduced? Because I'm having a hard time figuring out where that would happen.
Let's see how it could have happened...
1&2 Could easily have been just the Doctor and Missy.
3&4 Introduce O'Donnell as the new Companion but have the story set in the present rather than the future.
5&6 O'Donnell wouldn't have much to do / wouldn't have been in it.
7&8 O'Donnell had already been set up as being ex-UNIT so she'd have slotted right in. (Actually that bit of characterisation doesn't really make much sense in the televised story.)



Have you read the novel that the movie was based on?