Will the Reapers try to take it back if we saved the base in ME 2 or rebuild it if we destroyed it? They will need to build more Reapers afterall and even though there are no more collectors they can always turn in a new species into collectors.
We dont know the collector vermin have been completely exterminated. They could have a base elsewhere. Hell, they could be at the heart of every galactic core for all we know.
I wouldn't doubt that they have bases tin parts of the galaxy that have yet to be explored.