JMB - Infectious conjunctivitis appears some years and will run through your flock, then it may not appear again for several years. There is little point in segregating the affected sheep other than to make catching them to treat them easier, and to ensure they can find their water easily. Once everyone who is going to get it has done so, the flock will have a degree of immunity. The condition can be vaccinated against, but vaccinated animals act as permanent carriers, so if they then join with unvaccinated sheep, they will go down with the condition.
The usual way to treat conjunctivitis is to apply Orbenin once or twice a day for a few days (pull out the bottom eyelid when applying it so the whole eye is treated), by which time the blindness is usually improving. If it doesn't improve, or becomes worse and the eye gets a thick covering over it, then give the appropriate antibiotic - I use Terramycin LA given intramuscularly and this has always been effective for me. I have never used the injection into the eyelid out of pure squeamishness
but I believe it is as effective as an IM injection.
Conjunctivitis might be spread by flies, but please before you start spraying Crovect
on unshorn fleece, check that this is the case. Can you see flies around your sheep's heads? You may need to clean up their eyes anyway (bathe with salty water) as they tend to weep with conjunctivitis.
The reasons for not using a product such as Crovect on unshorn fleece, for three months prior to shearing, include the danger to anyone, including the shearer, who has to handle thousands of animals in the course of his job. The chemicals (neurotoxins) in Crovect, Clik and so on, can cause serious illness in humans exposed to them, and in someone who is sensitised, the illness can be severe. As your shearer has asked you not to spray before he comes to shear, it could mean that he is already sensitised.
Another reason would be to protect those handling the fleece, such as Wool Board sorters and craft workers, or judges at shows handling treated animals.
Thirdly, when fleece is scoured, the waste water has to be disposed of in an environmentally responsible manner and must be free of all dip and spray residue, as the water will be returned to a waterway. Removal of the chemical residues is expensive. Remember that these chemicals are toxic to insects so must not be released into the environment where they can do untold damage - as did DDT in the past.
There is no point getting into a blind panic about flystrike. Make sure your sheep are dagged and clean at all times - the flies are attracted to dung, although they can go for clean animals too.
You can treat your lambs with Crovect from the end of May, or earlier if there are signs of the greenbottles, repeating every 6 weeks.
Observe your adult sheep very carefully at least twice a day for signs of being bothered by flies, or struck. If you do get a problem, then treat that sheep, but mark it so your shearer knows it has been treated, then destroy the fleece afterwards, through the carcase disposal service.