My buddies and I had a "situation" today. I was attacking a hex with an ancient and my buddies' (Draco) cruisers. My plasma missiles knocked him off the hex.
Do I still get to fire my missiles once more, at the ancients? That is, are the ancient battle and the player battle considered separate battles? And if so, do i carry the damage with me until the end of the combat phase?
From the top of my head: Yes and yes.
I looked this up because your answer seemed logical (reloading missiles takes less time than repair) but I thought I remembered the actual rule being counter intuitive. Happily your answer seems to be supported in the rules. From page 18:
In the Combat Phase, battles are resolved.
If the hex contains more than two players' Ships, battles between players are resolved two players at a time, in reverse order of entry into the hex.
So the combat phase contains multiple battles and multiple players in a hex counts as multiple battles. Then from page 20
Every battle begins with Ships firing their Missiles (if any) once...
which suggests that missiles are fired once per battle, potentially multiple times per phase. Page 21 states that repair happens at the end of the combat phase, so damage would carry over between battles in the combat phase:
REPAIR DAMAGE At the end of the Combat Phase, all the Damage Cubes are removed from the Ships.
So this seems pretty much like common sense. Unless of course it has been overridden by an official response somewhere...