This sidequest is complete, but the complete story about the Darchlight Manor is not. You may want to complete the quest that starts, iirc, by visiting the Goldenleaf Gym/Theatre after winning against Narcissa.
AS it has been said, the girl in the pkmn center is part of a sidequest, so it's not necessary to advance the main plot. It's advisable to do, though. The girl you should be looking for spawns in one of the buildings/houses near the eastern train station.
In the same folder you found that one. You should find the 532 and all the way down (maybe not all 500, but you get me). Rename the most recent to game.rxdata and you can change it and use it.
First time I tried to just brute force my way through it with generic strategy and costed me a ton to win. Second time, I got my hands on Cosmic Power (happened to be on Solrock, but, you know) and it was walk by the park, if only time-consuming.
I think Beldum for the bug-ish method and torchic for the same, being the same with Mimikyu mainly because you don't get any hints of those methods. Gible isn't so difficult imo because you can have Taka with yourself who kind of helps you or hints it, Spiritomb is also doable given you got the Odd Keystone you know what is it for. Poipole isn't as difficult as time-consuming since there is a clear good prize to the sidequest and you could (in theory) be traded all the items needed.
You can purify the poisoned cave using the move called, well, Purify. It's Pyukumuku's signature move. Iirc, the move itself doesn't need a non-volatile status condition to change the environment.
A brainwashed victim?
I also miss the old good days when everyone was pretty much fine and not saddled with all the trauma... Except Keta, one would have to go further back for him
Given her umpleasantness they might even put her as Reborn City mayor just so she scares the rest of citizens away lol
Come to think of it, we may have guessed what the ideal Team Meteor plan would be. A shame Sirius/Solaris are such life-stopping enthusiasts.
I have to say I have seen this guy clearly for the first time as I have not played its games (...yet?) and its sprites doesn't help at all. So very glad to see it included!
My main concern about Lin's death is whether she's alive or not to begin with (?)
I think Solaris may also die, depending on the route (opposite to his son) and I think some of the good guys is going to die too.
She stayed in her home dimension/Timeline where she was not rescued/kidnapped/awakened by Team Xen and given to Prof. Jenner to take care under the name of Melia, probably. I also guess she did face a lot of trouble because stalling for mere seconds to indriad to save a few friends is very different from actually facing him.