While many might tell you that you have nothing to lose by trying, let me share what happened with my first agent. She would kindly give feedback as she passed on requested manuscripts, and then get more emails from the grateful writers. She tried putting on her agency site that passing means NO and to only query with new material, but to no avail. As she put it to all her clients when she finally closed all doors to new subs, "writers are so grateful to get any feedback they think this is an invitation, and I am overwhelmed."
I'm no longer with that agency and now am happily agented elsewhere, which is unrelated to any of this. But noted that my first agent continues to be closed to new submissions. So maybe there is something to lose. Not you personally, but for others.
This is what I would do if I were in your situation: continue to query to others while writing something new. When you have something new to query this thoughtful and helpful agent, if you are still not agented, do so. You could then mention her helpfulness in the past and that you took this agent's suggestions. See then if you really "rang her bell" so to speak and something comes of that.
No matter what you do, good luck and kudos not only for getting such personal guidance from a professional, but for following it and making the manuscript stronger. It's all good.

.