I was able to render the scene without applying the modifier before but after some fiddling with the smoke material, some weight paints in the scene, and rebaking, the smoke stopped appearing on the final render. It only appears again on the final rendered image after I hit apply to the smoke modifier. The problem is when I apply the smoke modifier, the smoke becomes more intense and seems to take the shape of its domain.
Update: Okay, it seems like the smoke will render and stay intact if I just apply the flow object modifier but I would still like to know why it stopped rendering before I apply the modifier