For every book you've ever read, chances are there are several versions of the story stacked away in the author's closet. I know at least there are for the books I've written. In some cases, there are entirely different novels with little resemblance except the main characters. That's the extreme however. Mostly there are just a handful of deleted scenes and alternative endings, much like the extras packaged for a movie's home release.
As I make my way through the second draft of the manuscript I'm working on, I just conquered a section where I decided to completely rewrite things. The action in the original manuscript was kind of a mess. Everything felt rushed, and it lacked the drama I had envisioned. That said, many of the plot points were right on target...they just needed to happen in a completely different way.
As a much younger writer, this would've been an incredibly frustrating realization, enough to possibly make me abandon the project. I didn't feel that way at all with this story. I actually had fun writing the additional scenes, knowing I was sending the characters on a much better adventure than the one they'd been on the first time around.
I'll admit that there's a part of me that loves those deleted chapters and dropped story lines. They're a way of holding onto a story even after the world gets a hold of it. As the writer, you're the only one who knows the events in the story hadn't always happened that way, making sure the first draft will always remain a secret you share between you and your characters.