Caterpillar viruses are reasonably specific and most of them turn the larva or caterpillar into soup. It would be odd, but not impossible, for a virus to infect two such different species as a monarch and a fritillary or swallowtail. The description and pictures fit a protozoan called a microsporidium which commonly infects across family lines in the butterflies and moths. These can also be transmitted vertically, from mother to offspring. The monarchs have their own particular protozoan, a weird one that comes out through the cuticle with the scales on the body and then is left on the host plant when eggs are laid. Larvae eat the spores while feeding and so the infection is perpetuated. The monarchs in the Texas flyway are reputedly about 15% infected with this species (Ophryocystis elektroscirrha - what a name!) and queens are also susceptible. I don't know if it would do this to a chrysalis, but the regular Nosema brand of protozoan would.
Another possibility is a bacterial infection brought about by stress. Was the emergence cage outside and did it get overly hot? Did the caterpillars get stressed before pupation, meaning something like running out of food for a day or so?
Lastly, it may not even be an infectious microbe that did this but rather something (like a chemical) on their host plant. Also, is there a chance that all the affected group came from the same parent? If the parent had a problem, it could show in the next generation.
If it is an infectious agent, you are doing the right thing. A 10% solution of chlorine bleach will kill any microbe of importance. So will sunlight - the UV rays are very effective at destroying all the caterpillar pathogens and do it within minutes. Take a stiff brush to remove the silk chrysalis attachments and to work the bleach into cracks in areas like boards or plywood lids and into any areas sunlight might not reach.
However, the emergence cage is probably not the problem, but rather the rearing cage or host plant. Except for some mostly soil-borne nematodes and a few fungi (and these pictures don't show evidence of that) all the pathogens have to either be eaten, passed from a parent or injected by a parasite in the larval stage of the butterfly or moth. Disinfection is by the same methods, with the addition that small things like vases and jars can also be microwaved. Ten seconds at high power kills all insect pathogens provided they are not protected by a layer of dirt or some such.
If this continues, save some of the dead pupae and chrysalises and I will put some wet mounts of tissue under a phase scope to determine whether or not a pathogen is involved and which one it is. The disinfection routine would still be the same, but at least you will know which one you're up against or whether there is something in the physiology to consider instead.
FM
