Hens having an egg break inside can be a fairly common occurence. I have seen it in hens who a year or two later died of egg yolk peritonitis. E. coli is an opportunistic bacteria present in the gut of all chickens. It can become a problem if there is an immunity problem, if there is a respiratory disease where it can spread through the air sacs to all parts of the body, or up the reproductive tract into the abdomen to cause peritonitis. There must be some sort of immunity problem in the birds who have died. I will be interested to see your final necropsy results. Lymphoid leukosis and Mareks are bott common diseases where there will be problems with immunity, but worms and coccidiosis can contribute to that also. Many of us never get droppings checked by our local vet for worms or cocci, but probably a good thing to do. I hope your flock's luck starts to get better soon.