Over at DeepGenre, a blog about writing by various published authors, Kate Elliott has a post about story plots changing. http://www.deepgenre.com/wordpress/kateelliott/craft/changing-horses-in-mid-stream#more-279.
This has happened to me, as well. For me, I try with each new story to have a better grasp of the overarcing plot, and I try to be a few chapters ahead in terms of main actions and plot. In book C, that I was working on last night, I am on chapter 2, but I know where I'm going through the end of chapter 3. Well, that's the plan anyway. I've never been that great picking out a chapter break. But I have the next two or three big plot points. What occurs with me, though, is that, often in the course of my writing group, someone will ask a question that makes me rethink a point. I'll decide that the opening chapter needs to change, or a strong character trait needs to be rethought, which affects later behavior, or a motivation will reveal itself for a character who I knew had a motive, but I hadn't yet put it into words (that amorphous feeling of 'I know why he's doing this, but let me try to put it in concrete words'), which give me a new insight to earlier actions.
My response is to usually make a note of it in a journal specifically for notes about my stories (I have many many journals, I would use one per book/series, but I keep jotting notes on scraps of paper, too, so I don't think I'd fill the journals up and I hate a waste of paper /tangent). Sometimes on a hard copy with other edits, sometimes in bold on my computer file. Then I charge forward with the sense of 'remember that so and so is now X'. I would go back to the beginning, I think that's a fine choice for some people, and rewrite the opening with this new information incorporated into the plot, but I don't for a couple of reasons.
1. If it happened with one plot-point or one character, it can happen later with another. I start writing with an incomplete picture and that becomes better defined the more I write, so by the end of the first draft, I usually have a list of big changes and new scenes to add in the earlier chapters. Why go through the extra work of changing the whole beginning, only to have to do it again later?
2. I don't want to get bogged down in editing the first three chapters. I know those will be important when I query agents, as, if they like the query, most ask for a partial of the first three chapters. But if I get to chapter 3 or 4, see a new direction for the story and go back to page 1 to rewrite, then rewrite up to chapter 3 or 4 and find another big direction change, and return to chapter 1 again, I worry that I'll never finish the first draft.
I had a professor (with 7 or 8 published contemporary fiction novels, so I found him to be a reliable source) once tell me that finishing a first draft meant the book was now half-done. Because revisions and edits were equally as important as writing it for the first time. I was really happy when I finished the first draft of my first story (although it's simmering on the back burner now, waiting for a overhaul revision), but I knew it had a ways to go before I could send it to an agent. Even now, I figure that it won't be the first book I try to get published. But I have a sheet of paper with notes based on comments from my professors about what changes I could make. It wouldn't be done now if I didn't just sit at my computer and type.
Happy writing, all. And may your stories take interesting new directions.