I had a nightmare summer when my mixed ewe flock got eye infections that kept doing the rounds and lasted about two-three months. They had contagious opthalmia and it caused the eyes of some of them to completely cloud over blue to the extent some were blinded and quite distressed
.
Initially I rounded them all up and gave them AB injections and put Orbenin ointment into the worst ones, not any easy job with a sheep who won't comply
. The infection seemed to clear but to my dismay some of the sheep that had got better, got reinfected! One of them had it so bad I thought she'd lose her eye. I did research over the net and found that treating them with ABs had limited use and that generally the disease ran it's course - which it did. It was quite worrying at the time but even the one whose eye was very badly affected totally recovered. I didn't bother any further with the ointment as it seemed to have no effect and most of it ended up on my hands rather than in the eyes, and I couldn't justify the cost with the amount of sheep I had!
Interestingly it was the coloured sheep, the Gotlands and Zwartbles who were the worst affected, the white sheep seemed hardly bothered by it, just one or two runny eyes.
I don't know if this was the same thing yours have got but all I can say is from my experience they did all recover 100% without further treatment, although it took some time.