"I've made some changes since I queried Agent X. Should I write to her about the new version?"
They queried too soon. Here's when to query: when you have spent so much time rewriting and editing that you cannot find one more significant (or insignificant) change to make. If you are still reading through your manuscript and still finding problems or things you can improve, it's too soon.
I understand the urge to get your work in to an agent who is willing to consider all comers, but resist. Wait until your new agent's notes will make you crazy because OMG, you know that book is PERFECT!!!