Yes, if the thinset is firmly attached and moderately level, you can add more then attach the cbu. BUT, keep in mind the original layer may crack and because it is hard, make it really hard to get the cbu to lay flat without voids. The whole reason for the cbu is two-fold: make a compatible bonding layer for the tile and decouple with the floor beneath. The reason for the thinset is to ensure 100% support.
If the thinset is fairly smooth and level and properly bonded to the subfloor, I'd consider installing Ditra from
www.schluter.com over it. This is relying on the thinset to hold it in place so there'd be no likelyhood of cracking the old, hardened thinset when you add the screws or the nails. If the existing thinset is NOT firmly bonded, though, there'd be a compromised connection holding the Ditra in place.
A rubbing stone could probably take off any high spots. It's better to remove it, though.
In the end, though, it might be less time consuming to just replace that layer of ply with new - less time, better end result; known condition.