She is! It's... possibly the single largest spoiler of FoE, that Fluttershy is still alive over 200 years past when she should've died, but yes. She was turned into a tree by Killer Joke (poison joke mutated into something quite vile by radiation) and it was only through the efforts of Velvet Remedy that Fluttershy was restored. She's... troubled, and has a lot of issues to work on, not to mention substantial amounts of survivor's guilt over so many different things(such as the entirety of Equestria, given some could argue she was the reason it perished in balefire to begin with) but she's alive.