Eric...this is really something for Steve.
My take on it is (if it is correct I haven't a clue):
Ship 1 is targeting fighter A. Missiles launched from the group including Ship 1 destroy fighter A, but some missiles Ship 1 fired remain. Fire Control on Ship 1 is now without a target. Missiles remaining at the end of the turn will use onboard sensors to switch to the nearby fighter B as they can see it.
Next turn Ship 1 targets fighter C and launches new missiles. Those missiles target fighter C, the other missiles target fighter B as they are self guiding at this point.
I would assume that once the seeker head on the missile activates to control the missile the fire control of the launching ship is no longer relevant. While it could go either way it does sort of defeat the purpose of putting sensors in the missile (baring the fact that without them they would self destruct) and it means that it doesn't matter what level of sensors you put in so long as the launching ship acquires a new target the missiles acquire it. But that is all...best guesses and may have no resemblance to the code.