Actually, the official site does not say anything regarding that, trackers claim that the movie is a sequel to the second season so far. It will remain as it is and it will be monitored for changes.
I have watched both the first season and the movie and the season which is airing right now picks up where it left off in the movie.
I checked and some sites including AniList do state that the movie isn’t the prequel to the current airing anime, I think so this is because of the events occurring differently in the light novel. So, don’t change anything and also add the movie to relations under the second season’s anime page.
I think that movie is rather a sequel cause in movie they did know Lina and they knew that she’s STARS agent. In this (second) season at start they didn’t know that. But that’s only my speculations and I can be wrong.