So you're a sailor with Vasco de Gama making your way from Portugal to India in search of "Christians and spices." It's been a long, fairly dreary voyage as you have yet to find substantial amounts of either. Your last several months have been filled with alien cities of Muslim Moors and African Pagans, heathens of all manner, but you know India is different. Christian literature recorded that Thomas went to India and converted massive kingdoms and legends of Barlaam and Iosephat have made their way to you, everyone in Europe knows that beyond the Ottomans and Persia lies India with its vast Christian kingdoms and plentiful spices.

And once you get there, lo and behold there are tens of thousands of Christians in Calcut, the first Indian city you find. You are able to make contact via traders who speak Arabic as you have brought translators from Tunis. Though their manner of dress and ways are alien to you, you know they are Christian by the way they trim their hair or let it grow wild and sing praises to God. The legends were true!

So you return to Portugal and tell of the way to India with its Christians and Spices. Perhaps you return on the next Voyage to establish a permenant prescence of Portugal in India in 1500 under Pedro Cabral. In the late summer you land in Calcut again and set yourself up with a local king, who calls himself a Nair. You are prepared this time, Vasco de Gama kidnapped, ahem aquired, some locals last time to serve as translators, so you can communicate directly with the king. You all get in his favor, take out a rival or two and establish yourselves, but by December are in low spirits. You decide to stick it to the competition, they're Muslims so it's okay. Unfortunately this causes a riot leading to the deaths of fifty crewmates. In retaliation your captain tells you to kill the Moorish merchants, so you do. However, you are incensed at this Nair King, is he even a Christian? How did he let these riots happen? So your captain orders the city bombed.

Well that went well, where there was once a thriving seaport, there is now only a ruin. Problem is you probably won't be doing buisiness here anymore. One of the captives suggests you head to Cochin, who warmly welcome you since you kind of, sort of destroyed their rivals in Calcut. However as you observe the strange ways of these "Christians" you begin to wonder how they have diverged such. Perhaps some paganish or Muslim customs have corrupted them.

While in Cochin you receieve missives from a few other rulers. Notably one from Cannanore. Seeing limited spices here, your captain orders that you sail there. You do and find that, hang on, there are a bunch of Christians and Jews here, praying at recognizable temple and reading Bibles, talking about Jesus and Saint Thomas, but haven't you been dealing with Christians this whole time.

Well, no, you are informed that you have in fact been dealing with Hindus. Hindus? you ask. What are those?

Pagans, you are told.

Well this certainly explains a lot, you think. And it does. But now you have found the Christian Kingdom of India, except, well it is ruled by a Hindu and dominated by them. In fact, much of India is ruled by these Hindus, all that isn't by Muslims. You are told of yet even stranger religions in a place called "Ceylon" where they worship some "Booduh." In any case, at least you found the Christians...

In any case, you head home, spices and a few local Christians in hand, to report the success to Portugal. Except the voyage was a disaster, Calcut hated you, you lost 8 ships, and found that the temples of India weren't just misguided by time separated from Rome, but pagan idolators. Though at least you had spices and found SOME Christians.

The next few missions are no less awful and are dominated by diplomatic failure and zealous massacres of Hindus and Muslims. Furthermore, once a number of outposts were established, it became clear that these Christians were Nestorian heretics. Their rite was Syriac and Mary was called "Mother of Christ" rather than "Mother of God." Furthermore, the priest married, practiced Indian exorcisms and Ayurvedic healing; very unCatholic. Despite this, the Portuguese establish friendly relations with the Syrian Church head, Mar Joseph, and made a somewhat subdued, attempt at inquisition. This lasted until Mar Joseph's death after which, one bishop was given permission by the pope to use theWest Syriac rite so long as he practiced Catholic doctrine while another was sent by the new head of the Syrian church leading to a schism.

You might find a partial answer in this post by /u/artfulorpheus: https://www.reddit.com/r/AskHistorians/comments/b3r1sd/why_exactly_did_the_church_of_the_east_vanish/ej3bsuz/?context=3

When the Portuguese sailed to India they were overjoyed to find a thriving Christian commu ity there and communion with the Pope and the remnant Syriac Church was established.

The Portuguese, however, were less pleased with the character of local worship, deeming "Nestorian" and pushing back against it. Whether the Church of the East was truely Nestorian is a matter for Christian scholars, but the relationship is complicated and coloured by Latin heresiology. In any case, this split the community between a number of factions, though the largest was (and remains) the East Syrian faction of the Syro-Malabar, who use the Eastern rite while in communion with Rome. The Faction remaining loyal to the Church of the East is much smaller, but still extant.