Noticed two things in a quick play with Beta 5.
1.When selecting the shipyard which is building the ship as its rally point it still spits the newly build ship out and sets it to idle.
2. After a starbase is destroyed the lines that connect to the resources being mined by the starbase remain leading back to the hex where the starbase used to be. I however didn't check to see what happens if you build a new base at a different location remaps it or not.