"Hi Noah, I have a question about querying that I haven't been able to find an answer to. After sending out a few queries, I received some advice that I really thought would improve my book. I took the advice and made some changes to my manuscript that changed the opening of the book (which I had already sent with some queries) as well as the length of the novel. Here's my question: What should you do if your manuscript changes after you've already queried? Obviously the MS is different than your sample pages, so what do you do? Thanks, ALC "
I wouldn't worry about this too much. From your post, first of all, it sounds as if you have only sent your queries out to a few agents. Typically, it takes sending a query letter out to dozens and dozens of agents until you land one. It is a numbers game. Chances are that you will not land an agent based on your small initial round anyway. So if the work that you already sent them is not in the best shape, there is not much you can do about it now, but I wouldn't worry about it too much, either.
If you were to contact these agents again with the revision of a query, it would likely be perceived that you as an author are too high maintenance. An agent does not wish to take on an author who is constantly submitting them revisions and never happy with the work. I have seen situations in the past where some authors will never be happy with their books, and revise endlessly, all throughout the process, even going right up to publication day, driving their agents and editors crazy. While you do want the best work you can have, you don't want to be perceived as one of these. It is too much work for everyone involved. At a certain point, you have to lock it down and be happy with it. Of course, the very nature of revision demands that we will never be happy with our works as authors. Which is why this is even an issue to begin with. At virtually any point in time, any author could look back at their work and want to make changes. At some point, we have to move on.
The other issue here is that, if an agent likes your general concept and genre and bio enough, presumably the agent would be intrigued to see more based on your initial query letter. If you made some minor revisions, that shouldn't impact their decision too much anyway.
Also be wary in general of making revisions based on a single agent or editor's comments. Publishing is a very subjective business, and if you change your manuscript to suit one person's needs, you might find that the other agents or editors would have preferred it the way it was originally. It is good to listen to people, but it is good to trust yourself, too.