If the stallion is a shedder, then he sheds the virus in the semen. That's what a "shedder" is. If he sheds the virus, he can't be "semen negative"... Someone needs to get their wording straight!
He may be "seropositive, semen negative". That means that his blood shows antibody presence against EAV (the virus is "EAV", the disease is "EVA"), but there is no presence of the virus in his semen. If that is the case, he is fine to breed an unvaccinated mare to. Stallions (or any horse) that have been vaccinated will be seropositive.
I'd get a definitive clarification before you go any further. If he is a shedder (i.e. virus in his semen), it would be undesirable to breed a mare with a foal at foot.
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