While I was occupying an empire (like I was doing subjugation to make them mine), and my starbase design upgrades finished all the systems I was temporarily occupying had all their star bases destroyed.

Also, this was after I loaded another save as when the designs upgraded and there where ships being built in one of my starbases (cough 30k worth of allloys cough) it canceled all of them without refunding the ships.

Edit: and it seems to have made research stations and mining stations around stars stop collecting. They are there but they don't harvest the deposit.