By "after the battle", you mean after she finishes her spell and teleports the ship to the Hall of Echoes? And by "was/wasn't there" are you talking about her showing up in the Hall of Echoes? You also said that you reloaded and she did appear, right? Then... you can just progress normally, no?
Someone did report that Malady was missing in their game at this part because they teleported her onto Dallis' ship during the fight. I'd wager that there is something that caused this issue in your game, and it can be prevented. Generally it's best to not touch her, except maybe healing or fortifying her.
