Link probably never parts with the Wind Waker
I mean the only reason why he didn’t have it in Phantom Hourglass was because that was in an alternate realm. And lets be real Link didn’t have his equipment on him when he was jumping after Tetra on the ghost ship.
So I like to think that Link just, keeps studying how to use the Wind Waker. He of course has the stuff he learned how to do while on his adventure but it’s obvious that it was made for so much more. So through his early adult life he probably learns a lot of extra tricks.
Like maybe not just wind direction, but wind velocity, so he can choose whether to summon a small breeze or a huge gust, or he gets warping to a point where he can carry Tetra’s whole ship (though its very uncomfortable for the crew so he probably doesn’t do it often).
I also imagine that as Tetra grows older she becomes more interested in her royal heritage than she was as a kid and gets really involved in piecing together what’s left of Hyrule’s history. She probably finds out at some point that the Wind Waker is either a spiritual successor to the Ocarina of Time, or just part of a collection of magical instruments used to communicate with the gods, and shares this info with Link.
Through all her studying Link finds the “language” that the Wind Waker uses and starts studying how to invent his own special moves with it. He starts experimenting on a small scale and eventually works his way up to being really powerful with it, like I’m talking wizard level powerful.
He learns it can do all kinds of weird shit, like it can pass more than just a day in time, but it can pass weeks, and even months. It can also go back in time, which maybe Link used once on a small scale, but decided that it was too big a gamble to really touch that aspect of it.
And then one day, he uses the command melody on a whole group of rival pirates… and it scares the shit out of him. Like, controlling the minds of a whole crew of people is probably too much for Link, and it scares him off even touching the Wind Waker for a while. Locks it away and doesn’t even want to talk about it.
At some point Link may decide that the Wind Waker is too big a responsibility and a terribly powerful thing that shouldn’t be at the beck and call of a mortal. He’s pure of heart and things probably wont go wrong with him, but he’s scared anyway, especially since he attributes his innocence to being a child at the time of his saving the Great Sea.
May not happen until they’re in New Hyrule, but I think Link would probably lock it away as an ancient relic and let the knowledge of how to use it’s more powerful spells die with him. But I like to think he’s making use of it while he’s on the seas with Tetra and the pirates, just giving them that sort of edge to their shenanigans.
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