I think most would have expected when the affiliation treaty was dissolved (by ferg subjugation of Angosia) the starbase would have been removed.Angosia is my affiliate, and I had a peace treaty with the Ferengi when they declared war on the Angosians. Eventually I declared war and liberated Angosia with one troop transport since the starbase was still there to ward off the Ferengi. Sadly, the starbase vanished after liberation. I'm guessing that's because the relationship status fully reset, though you would think that would happen right when the system was conquered.
I was the Cardassians, Fergs are AI
note; cards had non-aggression with ferengi (no combat with starbase by assaulting fleet)
I do have saved game turn before subjugation