5

If I clear a location in Fallout 4, it shows it as clear on map.

Does that location remain clear permanently?

If no, how does enemy spawning work in terms of time and difficulty.

8

Those locations do not stay clear permanently. For normal areas, it takes seven in-game days to reset. For "dungeons" (named quest-related locations that can be marked as "cleared"), it takes 20 in-game days (see this Reddit thread). These times scale with Survival difficulty — 35 in-game days for non-cleared areas, and 80 in-game days for cleared locations.

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