relay a has some set of notes relay b had another set of notes How do you sync these relays efficiently? Also from a client perspective: how do i query and download notes i don’t already have efficiently. No longer do we need to download tons of redundant data.

That's what HORNET Storage Scionic Merkle DAGs are for. I'm building the first relay that will use it btw, we are aiming to complete it in 4-5 months (that's our milestone target and funding limit).