This sharing of perspectives counts as understanding, and they return to their original bodies.

There was a brief flash of light, and when Link and Fi could see again, they were back in their proper bodies. "Master, it seems as though this counted as understanding!" Link told Fi.

Just as he caught what he had said, and how he had said it, Fi actually smiled genuinely at him, and giggled a little. "You are correct. We have a better understanding of each other now, and as such were allowed to return to normal." Growing more serious, Fi said, "Master, I apologize for my actions. I was crude, rude, and attempted to steal your body from you. I am sorry."

Link told her that he didn't much care. After all, being her was tough. They decided to not use the Crossbow of Souls again, after all the trouble it had caused. The experience had caused Link and Fi to be much closer to each other, and their bond made their journey easier. Some nights, in fact, Fi decided to "help" Link through some things that he had been willing to help her with, when they had been switched. By the time their journey was over, that inseparable pair were, in fact, separated, and the Crossbow of Souls was lost for a very long time. Not forever, though...

THE END

...or is it?