quick agent question about submission

That's a tough one, as you don't want the agent to think you sent her the MS before it was ready, but you do want her to read your best work.

I think if you do want to send her the new one, you shouldn't phrase it as withdrawing the MS. I would ask if she's started reading because if not you have an updated version following late beta feedback.

One of my friends did that and the agent was happy to read the new one. But I'm sure there are some agents who wouldn't like it. I think you have to weigh it up and decide whether the benefit outweighs the risk. Good luck!

Maybe say you're continuously revising, and after a short break you've had some fresh ideas and think they've made it better, but that if she prefers to see the one she has, that's okay. Or even just outline some of the changes in an email

I had a good experience with this. I wouldn't go into detail, just say you received feedback and are making modifications. You hope to have the modifications ready soon. Would they mind if you temporarily withdraw the manuscript and resubmit as soon as you are able. When I did this, I got very nice notes back.

I agree with Sage on this one. You want to avoid coming across as one of those 'flake' writers always chopping and changing something even after it's been submitted. They are hard work to deal with, and you do not want to come across as that.
You could certainly email and ask if they would rather see the revised version if they haven't started it yet, but I'd probably just leave it alone and see what they come back to you with.

I'm with Cam. Prolly shouldn't have sent it out to an agent while you were still beta-ing, but since you have, stand by that. And if she picks it up, you have a fab beta basis to add to, should she request changes.

ETA: IANAA

My own experience of this type of situation is different than yours, but as a cautionary tale, think it is worth passing on. I sent out a small group of email queries back in 2005, and by the time I woke up the next morning, a top agent in New York was calling me to offer representation. A couple of important things to note here are: 1) I had no idea this was a top agent. She was "an agent" from a list that seemed to match the type of material I had, but I knew nothing about her stellar reputation; and 2) I wasn't even close to prepared to be sending out a query letter, but was unaware of this fact. I had written out my book, a non-fiction book that belonged in the MBS category, and it was finished, as far as I could tell. This is what I said in my query. In addition to this, I wrote a very good query, something that I have always been fairly good at, thanks to my knack for salesmanship. I did sign with this agent, but then she was disappointed when I sent my draft, because it clearly wasn't ready. She sent it back, covered with what appeared to be hundreds of carefully considered notes. I took this as a request to make those changes and send it back right away--which I did--about a week later. This happened several times, and I think it exhausted the agent. After a year, the book remained unsold, so I cancelled the relationship with this agent. Since then, I have written four published books and five peer-reviewed journal articles. I also have a contract to publish my PhD thesis as a book with a major publisher of academic publications. What my later experience with writing has shown me is that it is very important to put your best foot forward, to not submit until ready, and then to avoid confusing the agent by constantly making changes--even if they are important to you. Best to wait until you have an established working relationship. Now, I am about to start looking for an agent again, but will be doing this differently and hope I am properly prepared this time.