When you take a pantheon, the pantheon belief will automatically appear in your existing and future founded cities (until you found a religion). But, once your pantheon is overtaken by another civ's religion in a given city, your pantheon can never reappear in that city.
The War Academy religion articles may help. This article is the intro and contains links to the more detailed articles.
The War Academy religion articles may help. This article is the intro and contains links to the more detailed articles.