Welcome, Steve
Here's the
Hardie-Backer installation instructions. They detail how to use their product in a countertop install
What you're proposing is not recommended and probably wouldn't work well. plus as you've already noted, it wouldn't look too great either.
So I wouldn't be too a'feared of ripping it all offa there, adding supports to maintain the min. 16" span, and building up w/ new ply such that your 2" BN plays nicely w/ the total thickness of plywood, backer, tile, and 2 layers of thinset. 3/4" (nominal) ply + 1/4" backer + 3/8" tile + 3/16" thinset puts you at about 1-9/16. So adding another 3/8" ply layer on top would work if you wanna. that would help the stiffness and to hold the BN better.
Keep your q's on this countertop right here in this thread and we'll do our best to help. Good luck w/ your project!