MacEachaidh - since you are going through the trouble of a reset and having to restore everything, why not just revert back to 3.12.0 since you had no issues on it? I'm surprised kobo said they would exchange your device for something that so clearly seems to be a firmware issue. I don't blame you for not sending it in. I don't think anyone had these issues with the long press on 3.12.00.
Good luck either way.