*minor spoilers*
The Garden of Seborin is the only area that really changes. At one point it becomes corrupted by Nightfall and turns all evil-looking with high-level monsters, and is an "interior" area like FoW or UW- meaning it has it's own U map, and mapping it doesn't affect the M map.
Completing the mission immediately after it (Jennur's Horde) turns it back to normal, as does beating the game (I think). This all doesn't really matter, since the best way to map the Garden is through the mission Tihark Orchard, which is available at any time.
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