If the attacking fleet wins the battle, it carries on to fight with the orbital fleet. If defending towers win the battle, this means that the attacking fleet was destroyed, and the fight is over.
After each fight, 70% of the destroyed towers are immediately auto-repaired. So, if you have, for example, two flights attacking a player, and the first one destroys the towers, the second attack will still have to defeat 70% of the initial towers, since these are repaired after each fight concludes.