It seems that although Nestorianism, or the peculiar Eastern Syrian Christology that was influenced by Nestorianism, was spreading among the bishops in Persia during St Isaac's time, still it hadn't yet become the official position of the whole hierarchy. There were still communications between Constantinople and the East that affirmed communion and common confession of faith. So St Isaac is held to have lived and died in communion with the Catholic Orthodox Church and may be venerated as a saint.
That's an interesting explanation. I am a bit surprised by it, though. From what I understood, the Persian (Assyrian) Church, unlike the Armenian Church, was not split between the two empires, but was rather pretty much contained within the borders of the Persian Empire. Therefore I understood that their hierarchy was not so fragmented. They were, in any event, pretty unified in their rejection of the Third Council and their condemnation of St. Cyril.
I do know that at the beginning of the seventh century, the emperor maurice put the EO Church back into communion with the Persian Church. Since St. Isaac lived during the seventh century, I always wondered if that was perhaps what made it possible for him to make it onto the EO calendar, as opposed to the OO where he is venerated but not officially on the calendar. I've never been able to find out how long that union lasted. I know it was not brought about by the Assyrians accepting the Third Council, but rather they submitted a confession of faith, which the emperor handed to his Patriarch for approval. I think the emperor wanted the union for political reasons and he was not the kind of person who liked to hear the word "no."
In any event, if the union lasted for more than a couple of decades, that may explain St. Isaac being on your calendar. I may get the book by HTM for myself, if it is not too expensive. I wasn't even aware of its publication. They have some pretty good stuff over there. Who knows, maybe what they say will help solve this question.