Should I mention this in query?

I would mention it, because otherwise she might wonder why you're querying her with the same project. Granted, she might not remember, but if you say nothing and she recognizes the plot or title or whatever, then she might just reject you out of hand.

Email! Seriously, you have this agent's email. You've emailed back and forth. This way you can more casually ask if she would have any interest, and I bet you hear back a lot sooner.

I would mention it, but low-key....

"you may not remember me, but we were messaging back and forth about two years ago--at the time, you thought my novel was good but destined for an over-saturated genre. I've revised the novel, and feel it is much stronger for it, and it is also not coming at such a time of plenty--I hope you'll have a look and agree" or something similar.

That's MY inclination, which won't be your only opinion or worth more or less than many of the others, but you DID have her interest once. I would mention it, but try to do so somewhat obliquely, so it didn't come across like you expected a free ride or anything, a la "hey, fucker, two years ago you said 'Two Moons' was awesome, but you had too many alt-world MG titles, and now you don't, so you kind of owe me......"

You could also email/respond to her using the last email she sent you. That way, she can scroll down and recall who you are and see by her own words she was interested. (I've done this many times and it usually works since it's basically using their own words to say, "See, you liked me one!"

I very strongly feel that you should mention that earlier correspondence. Going by everything I have read, such feedback is very rare. Good luck. I do hope it works for you this time.