The first time you see a shrimps exoskelaton it comes as a nasty shock, and tends to make you feel like its gone and died on you
. I wouldn't worry about her to much she will hide really well for a couple of days until her new shell is nicely hardened up, just like crabs who are easy targets after they have shed their old skin.
The rili's are so young it should be another month or two before they are capable of breeding, by then hopefully it will be easier to tell any males from females. I was thinking maybe you could breed the red to the rili's but as the offspring colour up only leave the rili patterned shrimp in the tank and rehouse the reds in another tank. At least then the rili gene shouldn't end up getting swamped and diluted by the stronger "normal" red.