Hi. The water crystal part comes before rescuing Serena and there's no way to skip some parts of the main story. Serena's rescue is a one-shot battle; after defeating her in combat, you can't return to that zone again.
I don't know how, what and why you changed in your save files, but it screwed up the game progression. It's a game-breaking bug and after two years from the release, I would've heard about this from other players. Since it's the first time I have seen something a mention about this, I can make an educated guess that it's a problem with your editing.