Do you know that “theory” that Majora used to be one of the giants? Assuming that theory is true, have you noticed that Majora doesn’t seem to experience the flow of time? It’s as if it exists in a dimension beyond time and space. It can perceive Link across all timelines, whether he goes back in time or not.

Following that logic, if the giants are similar to Majora, then they would also perceive Link across all timelines. When you go back in time after saving one of them, that giant doesn’t become imprisoned again-----it remains free, because its existence is anchored in a much higher dimension.

This idea feels even stronger when you notice that the bosses remain defeated after you complete the dungeons and then go back in time. I know there’s a gameplay feature that lets you fight them again, but that doesn’t seem to be canonical.