Could mass episode renaming be added to the series manager? There was a Trello ticket asking for it that was marked implemented when the series editor was added, but I don’t see any option to do a rename from there (on Windows) and doing it series by series is horrendously time consuming.
There is a Trello card for it: https://trello.com/c/RQRSdkhZ/432-rename-all-files-in-all-series Please vote.
There was a comment regarding it on mass edit, which is where it will likely end up.