Wind Waker's Missing Dungeons Were Put To Use In Later Zelda Titles

It's not new news that The Legend of Zelda: Wind Waker had missing dugeons. Aonuma has came out and answered why those dungeons were not included in the HD remake and here's what he had to say.

“I’m aware that lots of users wanted those two missing dungeons to be implemented in Wind Waker HD. But to be honest, we’ve already used those two dungeons for other titles after Wind Waker already. So right now, technically, they don’t really exist anymore…”
“We didn’t exactly use them as-is and implement them into another game. We’d add some [of their] features to other dungeons. So they’re in different dungeons now.” Elements of them must have found a way into Twilight Princess and Phantom Hourglass, but who knows – their remnants may be somewhere in Skyward Sword, too.”