Ask Impa what to do.

Link told Fi that the best idea would be to head to the Sealed Temple, use the Gate of Time, and talk to Impa. She was sent by the Goddess, after all, and might know something about the artifact.

In response, Fi nodded. "Of course, Master." She stood there for a few minutes, Link floating there, before finally adding, "Master, how will we get to the Temple?"

If it was possible, Link would have rolled his eyes. He replied that he would fly them there like usual...then he saw the problem.

It took a lot of coaching and trial and error for Fi to get them safely to the hole in the clouds and down to the surface. She may have been an ancient spirit with more knowledge in her head than anyone alive, but she had no experience with having a human body, let alone using it to fly a loftwing. As they approached Impa through the Gate of Time, Link floating behind Fi, he could see immediately that she knew something was wrong. For a second her body tensed, ready to defend Zelda, but then something clicked and the tension vanished, replaced with...amusement? "Fi...is that you in there?"

"Affirmative," Fi responded, holding out the crossbow. "My Master found the Crossbow of Soul's and used it on my body, as an experiment. We have yet to determine a solution that leads to both of us returning to our appropriate bodies. My Master assumed you may know of a way."

Impa looked at Link, a rare genuine smile from her on her face. "Link, that's you, huh?" She actually let out a small, quiet laugh. "Well, I do actually know a bit about that magical device, since my people invented it. From what I remember, you two can switch back..."