Well her mission was kinda done, and being a simple clone she really had no other point in life. Perhaps she showed interest in Serge (though it was very hard for me to understand what exactly she wanted. It seemed like she was in love with Serge but then again it didn't.)
I think Harle's character was meant to represent the duality, so present in the whole game. My interpretation is that her origins are both of a human (Schala) and of a dragon/dragonian, two opposites, and that makes her not want to follow her mission and love Serge, though she can't. I think her scene with Starky on SS Zelbess show that very well. She's crying because she knows she will have to destroy Serge and anything else she might love in the human world.
The idea is that her purpose goes against her nature. Thus, she's divided and frustrated
There are also two other scenes that might say something important about her. One when she talks to Serge in front of the Pearl Gates. Another when she's about to catch the Flame at Chronopolis and has a dialog with Kid (I can't tell now for sure or in details, but it seemed like they could have inverted roles or read one another's minds).
I presume she merged with the Dragon God after all. Or she just disappeared in thin air because she had no purpose anymore. Maybe the Dragon God made her vanish.
Well, if she vanished after retrieving the Flame, then she wouldn't appear in that ending when humans were banned from El Nido or something. This ending happens when Terra Tower has risen, right after Harle accomplished her mission. In the main ending, I believe she ends up probably alive, no matter where or how.
