Indian church was submitted to the Church of Fars- South Persia- as the Metropolitan was in Fars and the Bishops of India were suffragans. It was the Metropolitan of Fars-Rewardushir who was to consecrate Bishops for India. We can see in the history that the Metropolitan of Fars sending liturgical texts etc.to India.
It seems that at some point, the Metropolitan of Fars refused to consecrate Bishops for India. Therefore, Church of India was without any Bishops. This led to elevation of the Church of India to a Metropolitanate so that he can consecrate Bishops for India and he will be directly under the Patriarchate in Ctesiphon and not under the Metropolitan of the Church of Fars.
The following quote seems to show that the reason for this refusal to consecrate Bishops for India was simony.
Patriarch Isho Yahb III (650-660) writes to Simon, the Metropolitan of Riwardashir-’ Remember with these, O our God loving brother , that as you closed the door of the episcopal ordination in the face of the many peoples of India, and you impeded the gift of God for the sake of perishable gains which kindle the passions of the body’…… ‘ as far as your district is concerned, from the time you showed recalcitrance against ecclesiastical canons, the episcopal succession has been interrupted in India, and this country has since sat in darkness, far from the light of divine teaching by means of rightful bishops: not only India that extends from the borders of the Persian empire, to the country which is called Kalah, which is a distance of one thousand and two hundread parasangs, but even your own Fars’(Mingana, early spread of Christianity in India, citing Assemani and Liber Epistularum).
There was indeed a kind of dispute between Church of Ctesiphon and the Church of Fars. The reasons for this could be,
1 Church of Fars, as well as Church of India, was founded by Saint Thomas, the Apostle, while the Church of Ctesiphon was founded by Mar Mari, one of the desciples of Saint Thomas, the Apostle. Bar Hebraeus wrote, ‘They ( Church of Fars) used to say, we have been evangelised by the Apostle Thomas, and we have no share with the See of Mari’ This argument is very important as why should the Christians evangelised by Saint Thomas the Apostle himself, submitted to another See founded only by a disciple ? ( Mingana, Early Spread of Christianity in India). This could be the earliest statement that shows a claim that we are Christians of Saint Thomas.
2 Political. Church of Fars used Pahlavi as the liturgical language while Church of Ctesiphon used Syriac as liturgical language. This could be due to political reasons. The Church of Fars might have adopted to the political requirements of the Sassanian Empire for survival.Thus, Church of Fars developed into a parallel ecclesiastical centre and controlled the Churches of Bahrain, Oman, Socotora and India, while the seat of the Patriarchate was at Ctesiphone.
It seems that during this dispute/schism,the Metropolitan of Rewardushir consecrated Bishops without the confirmation of the Patriarch and denied Bishops for India. Hence, Patriarch Isho Yahb III wrote five letters to the Bishops,Monks and the faithful, ordering them to reject the Bishops uncanonically ordained and reiterating the superiority of the Patriarchal See.( Mingana, Early Spread of Christianity In India)
Patriarch Isho Yahb III (650-660) and Patriarch Timothy I (779-823) tried to unify the Church of Fars back to the Patriarchate and prevented a schism. As mentioned before, Patriarch Isho Yahb III elevated Church of India to a Metropolitanate and thus the Indian Church became directly under the Patriarchate. Patriarch Timothy also reconciled with the Church of Fars by allowing the Metropolitan of Rewardushir to consecrate suffragan Bishops without the confirmation by the Patriarch. ( Mingana quoting Bar Hebraeus)