We have had 6 RIR since May of 2012 and things were going well. In February I decided to attend a swap and picked up 2 Barred Rocks that were about 6 weeks old I was told they were vaccinated. We kept them in the house separate from the other birds when one developed some sort of paralysis and after if worsened we put it out of its misery after having it for 6 weeks. I did notice a sneeze but it was only once or twice... didn't seem sickly until it started limping and then became completely paralyzed. Leaving one lone pullet... this was in April the lone survivor was placed separate but near the RIR for several weeks and we placed her with the established flock at night and they beat her terribly, I even stitched her head back together with needle and thread. So we purchased 2 Mottled Javas from a very reputable breeder near our town. These birds were his sons 4-H Project and had too yellow of legs. They were about the same age as the Barred. The first night we had the pullets in the outdoor secured yard and the original flock in their coop. Needless to say they huddled in a corner and a raccoon made dinner of the remaining Rock and 1 Java pulling them through the 2x4 welded wire fencing. Leaving us again with 1 single pullet. So once again I found and purchased an Auracana and Barred Rock. Somewhere around this time we noticed a severe drop in production. We were getting 5-6 eggs reliably every day like clockwork. Now I have banded the RIR and have found the following. 1 was laying shelless, even a yolk only, then deformed shells, then incomplete with holes on the end, now whole shells with watery albumen much smaller like a pullet would lay. One appears to have not laid any eggs for almost 2 months now and a third once a week... If it is any of the above diseases will they get over it? The other 3 RIR seem to be laying fine the new Barred Rock has started to lay and her eggs are small but normal albumen. There are no excess feathers that a molt would have caused. Sorry its such a long story... Any help would be appreciated. Thinking of putting the 3 down but if I get new pullets is the virus still there? What about the two that have yet to lay?