If you can't take it over as a workshop, it'll respawn. Enemies will reappear inside, ready to be slaughtered all over again and their bodies looted. Handy Fuel outside Super Duper Mart will always come back. I suppose this comes up because the game's map tags areas you've finished as 'Cleared'.
I've seen this asked dozens of times so thought I'd let my readers know that yes, like in other Bethesda games, enemies come back to locations you've cleared in Fallout 4.
