Dear Miss Snark,
I recently heard back from an agent I querried over 6 months ago who requested the first 3 chapters of my novel. (She apologized for the delay, saying she was only recently taking on new clients.)
However I've changed the novel considerably since that query letter was sent out so many moons ago. {The changes came after multiple passes by agents, as well as after my own epiphanies about how to improve it.) The novel still centers around the same main character, starting from the same situation, and essentially following the same character arc. But the path the character follows to his destination is markedly different, and the novel is more of a romantic comedy now. (instead of what?--thriller? dyspeptic parody of Jane Austen?)
Which do I send? The original version only? The new version only, w/ a letter explaining the change? Or do I send both with an explanation? Or would an agent view such a writer as wishy-washy?
I don't care how you got to good, I only care if you've arrived.
Thus, send your best work (in this case the new version), no explanations required.
Explanation of the changes you've made is akin to saying "gosh you look nice" to a friend and then getting chapter and verse on the gym regimen. I don't want to see you sweat; I don't want to hear about your sweating; I want only to gaze admiringly on your abs of steel.
If you just can't bear to let your improvements go unremarked, say very very briefly in your cover letter that you've been fine tuning your chapters between the time you first wrote and now when you are sending.