Wowsers, this is a tough situation. My first thought was to look at the rostrum, then I actually looked at the rostrum on my chameleons! Yeah that idea is out unless you have a dissecting microscope and time to sort them one by one.
Your largest shrimp would have to be RCS as chameleons dont get very big. Chameleons are the smallest shrimp I've kept and their shrimplets are tiny.
Chameleons are supposed to change colour but I'm able to pick the same individuals in my tank day after day, so I'm not sure if there is any way to differentiate them by colour or colour in response to stress.
It really is a difficult situation. I'm sorry I can't offer any better advice.
Best of luck.