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I think it's intentionally left ambiguous. Napoleon is simply "not there." There are several places he SAYS he is afterwards; however, he takes no true active part in the battle. The key thing to note is that afterwards, he uses Squealer as his "propaganda tool" to let the others know of his influences during the battle. In other words, he was probably hiding or watching, but in no way to participate. After all, if he was injured, what would the animals do then? It was essentially his way of manipulating the animals to do as he said and believe what he wanted.
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