It can. Under normal circumstances, when the stallion breeds a mare his penis penetrates into or even through the cervix into the uterus. This is not a problem when the mare is in estrus ("heat") as the cervix should be thoroughly relaxed. When she is pregnant however, (a) the cervix is not relaxed, so damage may result; and (b) in the event that he does manage to penetrate into or through the cervix, the pregnancy is almost certainly going to be lost - possibly following a placentitis situation (especially in later pregnancy) which could cost a fair amount of money to treat.
You are better off separating them.
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