Haven't used Custom Houses in some time, but isn't it possible to set it so it sells all but two horses? Alternatively, you could keep two horses in a wagon train while you sell the rest.
If you sell horses (or anything else) through a custom house there is always a minimum quantity of 50 retained. If you have 200 horses in a colony the custom house will only sell 150 of them so you will always have enough stock left to breed from. However the more horses you have the more you can breed, assuming you have enough feed for them.
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