They were back in their original bodies! They now understood each other.

...they both felt odd, and when they looked down, they saw they were in their original bodies. Link looked at Fi, feeling a little odd seeing his blue body from this side again. "Master, it seems as though our carnal recreation was enough to constitute 'understanding', and as such we were returned to our own forms."

Fi nodded, and told Link that it was actually really weird, being in a female body again. Or, rather, a female sword-spirit body.

Looking down at her now male body, Link felt uncomfortable. "I agree with you, Master. Even though I remember that this is the body I lived in for the majority of my life, it now feels alien to me." She looked at the Crossbow of Souls, thinking. "Master, if it pleases you, would you like to switch back? I personally find the idea appealing. My mind is too sharp and analytical to waste as the Hero, not when you are as well-suited to it as you are."