I am playing against the Vodyani and I have destroyed the same Ark a number of times.  It moved over one of my Star Systems and I destroyed it.  Now, every time they send 2 fleets to that location, I fight one of them off and the second one just drops some Dust and the Ark is, by some nefarious magic, fully operational and upgraded. This seems like a very broken mechanic that could be easily exploited.