If Link enters a scrolling side warp from a NES Dungeon Dmap to a screen with permanent secrets that have been triggered, the secrets are not triggered upon entry (but will show up as triggered if entering the screen again a different way. This is the same test quest as the walkability cheat bug report. The NES Dungeon screen with the scrolling warp is on the right. The screen on top is a NES dungeon screen without a scrolling warp set.
EDIT: It looks like dungeon doors don't work when doing a scrolling warp to a NES dungeon Dmap. I updated the test quest.