So I just went on a slicing-spree of all of the unused tiles in Dreams of Yesterday to see if I can reduce its filesize, (400KB gone. Woo.) I right-clicked in the tiles page, went to View->Hide Used. Awesome ability. Absolutely. Mind blown how it works, but it does.
... But it turns out that it seems to miss Link's Large Shield & Magic Shield sprites when using the BS-Zelda Link animation style.
Basically, it misses Tiles #8 through #18. It didn't think those tiles were in use.
EDIT: Addendum: It also tends to skip tiles that use the Combo Animation style "A.Skip".
The tile pointed to by the pink arrow there was still there when it was hiding used tiles.