Does obsessive doubt invalidate the fast of one making up for missed fasts (Qadaa’) by intending to break the fast, swallowing food remnants, or water entering the ear, for someone who suffers from it?

You did well by resisting the waswas (whispers/obsessive thoughts), and your fasting is valid. These waswas are inconsequential. It is obligatory for a person afflicted by waswas to disregard them and proceed with their worship. Their waswas hold no ruling. They should seek refuge in Allah from the accursed Satan and cease these obsessive thoughts. The person who is excessively doubtful—their doubts are not to be given any weight.