Make changes to Android Studio project exported from Unity

Let's suppose that I have a Unity Project, I'd like to Manage all navegation from Android Studio Natively, then I export the project for Android Studio and then I Import the project into Android Studio, I made the changes I consider in Navegation, Adding more Activities, etc. and now let's soppose I build my Apk and I post it into PlayStore. I'd need continue working on my videogame and navigation, so , If I make changes on my videogame, how could I vincule those changes in the existing Android Studio Project avoiding export a new one, what about versioning?

Thank you in Advance!

If I understand correctly you simply export from Unity to the same folder as previously, your files will stay intact, you might want to check build.gradle and delete the comment on the very top, so Unity wouldn't overwrite this file, as for other files, I think Unity doesn't overwrite them if they're present on disk