I have been reading Theodoret's attack on Cyril's Twelve Anathemas, and very surreal reading it is. Part of the reason for the strangeness of it is that Theodoret of Cyr was, without any question, a saintly man, a savvy theologian, a careful interpreter of texts, and a passionate defender of orthodoxy. He was also a passionate defender of Nestorius, who he seems to have misinterpreted, and a passionate critic of St. Cyril, who he definitely misinterpreted. The Counter-Statements to the Anathemas reads like a perpetual ignoratio elenchi in which Theodoret attacks an orthodox statement of Cyril by making an orthodox statement. For instance, in Anathema IX Cyril condemns those saying that the one Lord Jesus was glorified by the Spirit as an alien power and not His own proper Spirit. So Theodoret responds by vehemently insisting that the Lord Jesus was glorified by the Spirit. Well, yes, but hardly to the point, since Cyril's point was not that the Spirit does not glorify Jesus but that He does not do so as an alien power but as the Spirit of Christ. In Anathema II, Cyril insists that the Word is united by hypostasis with the flesh; to which Theodoret replies that the natures are not mixed. In Anathema III, Cyril claims that the union is a concurrence by nature; and Theodoret says that this is wrong because it was voluntary. It is true that the natures are not mixed, but, again, not to the point, since Cyril doesn't say they are, and it is true that it was voluntary, but, again, Cyril doesn't deny that it was. Throughout Theodoret assumes that Cyril is mixing the natures and attributing mutability to the Word; of course, interpreted in this way, Cyril would be heterodox, but nothing about what Cyril says requires this interpretation.
Another part of reading it is that it is a heretical text, condemned by the Second Council of Constantinople, in which every single thing in it might be taken in an orthodox sense, and very probably was taken in such a sense by Theodoret. This paradox makes it unsettling reading; but it is, of course, not a contradiction. Just about anything may be taken in an orthodox sense; it does not follow that every statement is easily taken to be so, and much of Theodoret's language is simply a confused and confusing mishmash that is easily read as disposed to heresy. This is not at all surprising given that Theodoret regularly defends Nestorian terminology (e.g., he talks of "the man assumed of us by God") in a sense that is in no way consistent with Nestorian doctrine; and this because he thinks Cyril's terminology is obviously Apollinarian. He's a verbal Nestorian, but he holds that Mary is Theotokos, that the Word took flesh and tabernacled among us, that Christ is one without mixture or confusion, and explains the phrase 'God assumed man' in such a way as to mean 'God assumed human nature'.
Theodoret's writings against Cyril are heretical in the material sense; but Theodoret later condemned Nestorian Christology, and became a rather vehement critic of it. In particular he seems to have been put out by the Nestorian denial that Mary was Theotokos. Theodoret had certainly always believed that she was Theotokos, since he forcefully affirms it in the middle of attacking Cyril, whom we usually think of it as the great defender of the title. And this seems to be typical of Theodoret's doctrine, in which he upholds an orthodox position and fails to distinguish it in a clear way from the Nestorian position. What a confusing time it must have been. In any case, Theodoret's censure against Nestorius was slow in coming; he went from defending Nestorius and his claims as orthodox, to accepting doctrinal reconciliation with Cyril (since he had misinterpreted Cyril as an Apollinarian, his view of it is that Cyril has stopped being Apollinarian) while abhorring him as a disturber of God's peace and refusing to condemn Nestorius (e.g., here and here and here), to rejecting Nestorius's claims as heterodox while refusing to condemn Nestorius, to condemning Nestorius.