Judging from the comments section on query tracker, it seems that plenty of agents will accept re-query if you query again at least 6 months later and tell them it has been heavily revised.
I'm very surprised to hear it. We never encouraged or accepted re-queries when I was an agent. In fact, one of the reasons we rarely replied substantively to queries was because it encouraged recipients to revise and resubmit, which we didn't want. The reason may sound a bit harsh, but we're into plain truths on this forum, right? It's because 95% of the time, writers would slap a bandaid over the ms., change a word here or there, respond narrowly to specific crits, and call it a day. The results would be no more publishable than before, and the writers would be angry and resentful when rejected for a second time. ("But I did what you wanted!")
There are a few writers--the best writers--- for whom good critique is like rain falling on parched land. It stimulates all sorts of new thinking about the ms and inspires revisions that the critiquer never even thought of or suggested. When you read the revised ms. of one of these writers, you encounter no patches or band-aids, and you can't even tell what the writer's done differently; yet the problems that were there before are no longer problems. Their quality shows in the original ms., so while we might turn down the ms as is, we would offer some specific critique and invted them to resubmit if they revise.
Otherwise, the chances that an unacceptable ms. will be made into an acceptable one are too slim to invest time in re-queries.
But if other agents feel differently, more power to the writer!
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