we found out our flock had CL, too. We vaccinate our lambs that we know we are keeping (most are for milk) at 8 weeks, and again 4 weeks later, and our ewes get vaccinated yearly. I don't vaccinate anyone who has obvious signs of the disease and we have not culled. We have a small flock, and they are good moms. Our vet told us that it doesn't pass through the milk, and that it takes months to develop, so vaccinating a lamb at 8 weeks usually does the trick. I have not seen, a year later, any of last years ewe lambs that we kept as breeding stock become infected. over time, we are hoping with vaccinations, that this will work itself out of the flock.
However, our vet said that 90% of the sheep in our state have it, so anytime we bring in a ram for breeding, we could be putting our uninfected sheep at risk. if any sheep have been vaccinated, there is no way to tell if they are infected or not. i know that's not helpful, but the vaccination is pretty inexpensive, so we are probably going to vaccinate for ever. Since CL can hang around in the soil and on fenceposts, we'd have to cull our flock and be without sheep for probably a year before we could bring in a fresh flock and start over - then the trick would be finding an uninfected flock in our area to start from!