After suffering major losses in ship battles, when I load the game to an earlier state (way before the battles), the ships that I lost do not get restored.  Also, damaged ships aren't restored either.

For instance, in the Drekneck system, I fought two battles - after the second battle, i was down 1 Tywom ship, plus 2 other ships were reduced to 50% crew.  I reloaded the game to when I first entered the system and found the ships and crew were exactly after I had fought the second battle.  This meant that I had to re-do the battles with less ships and crew!