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.)