Something like this happened to me a couple of days ago. I was happily intending to write the next section of "Ink" when I realized something crucial was missing. But to insert this change, I'd have to rewrite everything that came before it (only one long scene at that point, luckily) -- plus my thinking about the ending of the story would have to be retooled. Damn.
But late that night I realized this was a positive turn of events and not a tragedy at all. The newly inserted idea actually resolved a much bigger conflict I was going to have to face at the end of the book. (As I said in an earlier post, I don't work out all the details of my stories beforehand, preferring to wing it, at least partially.) So not only wasn't the new idea a problem -- it was just what I needed.
This is another example of living with your idea, letting it roll around in your head and allowing it to change and grow. Writing is an organic process. It lives, so it shouldn't be surprising that it exhibits signs of life. During the course of writing a book, I find the story weaves this way and that, bowing to the pressures of logic and storytelling. It goes where it needs to go, if I let it.
Don't let your plans slow down your progress. Adapt, and keep on writing.