After the rattler got in and ate the first two chicks, did you try to determine how it gained entrance and fix it? If the second two chicks disappeared, deductive reasoning leads me to conclude that a second snake took advantage of the entrance the first snake used to enter.
If you are under the mistaken notion that snakes are usually a single occurrence, they can sometimes be like mice in that when you see one, there can be plenty more where that one came from.
I live in a heavily forested area with widely scattered homes. Some of these homes are situated among rock outcroppings which make for ideal snake habitat. Snakes in such a habitat often reside in mating groups. Neighbors living among these rock outcroppings end up seeing several rattle snakes each spring and summer while I've been fortunate to have only encountered four over a span of 24 years.
In spite of rattlers being a relatively rare occurrence around my coops and runs, I've installed small mesh hardware cloth all around the lower two feet of run, and I've blocked the space under doors and gates with a rock sill. Finding a rattler in my run is an extremely unpleasant experience, and I'd rather spend time and materials to avoid future encounters if I can.
Good luck with keeping those slithering predators out!!!!!!
