Caves and crypts will not repopulate once cleared unless they had a 'generator' and you left it standing (for example the purple smoking bone piles in crypts).

The troll cave should be fine as no troll will spawn inside BUT I don't know if a workbench inside the cave would prevent a troll from spawning outside the little cave 'instance' so let me know if it seems to work.

Never actually tried to build inside one; can you even place a workbench? if you can it is kind of a neat idea and would be immune to raids.