Estius' claim that the Michael oratories were converted pagan shrines has no basis in Theodoret
Estius' remark is so absurd that it needs no refutation. He says that by the oratories dedicated to Saint Michael Theodoret does not mean places the heretics consecrated to their unlawful worship of angels, but places once defiled by the heretics' idolatry and later turned into oratories of Saint Michael by the prudence of the catholic bishops.
One would have to imagine Theodoret out of his mind to have him say what Estius maintains: that the old heretics used to pray to angels, the Synod of Laodicea forbade it, and therefore the place where they prayed to angels was changed into oratories of Saint Michael by the wise counsel of the orthodox. Besides, Theodoret does not hint at any such conversion of places, or at any such supposed prudence of bishops.
Theodoret's purpose forces itself even on unwilling readers. He means to prove what he had said, that the vice of those who called on angels lasted a long time in Phrygia and Pisidia, from the fact that down to his own day oratories dedicated by them to Michael could be seen among the Phrygians and their neighbors the Pisidians. No such oratories were found in the rest of the Christian world (Theodoret, Commentary on the Epistle to the Colossians, chapter 2).
Latin
LXXXVIII. Nam ita absurdum est, ut non egeat refutatione, quod observat Estius; nempe Theodoretum per Oratoria Sancto Michaeli dicata, non intelligere loca ab haereticis consecrata illicito suo Angelorum cultui; sed quae ante haereticorum idololatria polluta, tum temporis Episcoporum Catholicorum prudentia in Oratoria Sancti Michaelis conversa erant. Nam insanum oportet fingere Theodoretum, ut dicat quod pertendit Estius, haereticos veteres solitos Angelos precari, id vero prohibuisse Synodum Laodicenam, & propterea loco ubi Angelos precabantur, Orthodoxorum prudenti concilio, fuisse in Oratoria Sancti Michaelis mutata. Adde quod de ista locorum conversione & mutatione deque praesumpta illa Episcoporum prudentia ne hilum quidem apud Theodoretum innuitur. Legentibus vero etiam invitis, sese obtrudit Theodoreti Scopus, qui est probare quod dixerat, hoc vitium eorum qui Angelos invocabant perdiu in Phrygia & Pisidia mansisse, ex eo quod ad tempora usque Theodoreti ipsius, visebantur apud Phrygas, & finitimos eorum Pisidas, Oratoria ab ipsis Michaeli dicata. Qualia Oratoria in reliquis orbis Christiani partibus non reperiebantur. Commentar. in epist. ad Col. cap. 2.