You can’t highlight just one instance, but you can highlight the source mesh and all of its instances or you can also clone the source mesh and highlight just the clone.
For example to select instance 1 you can do something like: clone Mesh A, disable instance 1 of Mesh A, copy transform from instance 1 to clone, and add clone to highlight layer. Then when it’s deselected: copy transform from clone of Mesh A back to instance 1 of Mesh A, enable instance 1, then disable the clone and save it for next time one of mesh A’s instances is selected.
I only have single select in my little editor so far, so that’s as far as I’ve gone with it, but theoretically you can create an instance of that clone for each instance of A that’s selected, that way there’s only 2 draw calls total for all of the instances of A…
It’s the same for outline rendering too, instances are great for reducing draw calls but not as flexible as clones and sometimes the workarounds get a little tricky…
I am not sure exactly how you are planning to highlight. But if there is a glow layer involved, that requires multi materials in all cases, because the effect is layered. It boosts your draw calls by 3 (I think). But since you can change the emissiveColor per particle, that’s why I thought it might work for you. I have not done exactly what you are trying to do, but that is my understanding of how it works.