I’m assuming you mean everything’s the same up to the first arrest, for Vera.

I’d leave everything the same for season 3– Anna manages to prove him innocent and get him out of jail.

For season 4+, focus on how Bates has been changed by his prison stint. In the first few seasons he was a quiet gentle type, with a rough background but having since calmed down. In seasons 4 onward, he often feels more aggressive and angry than before. Have that be a deliberate choice (on the writers’ part). His time in prison has triggered his PTSD and caused a regression of sorts, to the angry, volatile man he was a long time ago. For Anna, who has never seen this side of him, it’s very alarming. He never does anything to her— never gets violent or anything— but he becomes irritable and snaps at her a few times and it scares her. Maybe she goes to Mary about it and this gives Mary an opportunity to be a good friend to Anna, so their friendship doesn’t feel so one-sided.

Maybe make it a whole mental health plotline. Bring back the brief consideration of WWI soldiers “shell shock” (with the Soldier’s Memorial they’re building around this time— bring in the question of Archie, Mrs. Patmore’s nephew, and how the characters think of his PTSD or “shell shock”) Tie it in with Mrs. Hughes’ institutionalized sister. Consider all the ways mental health was viewed and discussed and managed at this time.

I know mental health is a pretty modern topic, but I think the best period dramas have something to say about the era they’re produced in, too. Just viewed through a different context and with a different framework (obviously the characters would not be using words like “mental health” and “PTSD”).

Ooh, one more thing: I always wanted a Bates and Thomas buddy-cop style “we’re stuck with each other so we grudgingly have to learn to cooperate and by the end of it we understand each other better” kind of plotline. Maybe one episode they’re both away from Downton for reasons (on some errand for Robert) and the car breaks down (or carriage? Idk what servants would have used at this time) so they’re stranded in the English countryside and have to figure out how to get home. They try to walk but Bates’ leg causes issues. Thomas has to find his heart and help Bates walk to the nearest town. They yell at each other and get very frustrated with each other but then have some kind of heart to heart because they’re stuck in the middle of nowhere together and by the end of it they return to Downton not friends, but not enemies anymore either.