In one of my classes at a state university, I learned of two groups of Christians which preserved their culture while cut off from other groups of Christians. Although they were considered hidden or secret, there is still historic evidence that they existed. My source of information on this is the lecture of my professor, but I found a few links that have similar information.
There are Christians in Kerala India who claim, and have evidence, that they were converted by St. Thomas the apostle in the 1st century. At least, they were already practicing Christianity when Vasco de Gama found them in 1502, much to his surprise. I was friends with a young woman from Kerala several years ago, and she told me that she and her husband both came from very old Catholic families, and told me the story of how St. Thomas brought the gospel to India.
Here is a Kerala tourism website which matter of factly states their long Christian history.
For the native Christians, European missionaries and other post-medieval colonizers were late comers. Christianity in KERALA dates back from A.D. 52 when Apostle THOMAS arrived in KERALA (MALABAR Coast). St. THOMAS was one of the twelve apostles or disciples of JESUS CHRIST .
He is the founder of the Christian Church in INDIA . He was assassinated in MADRAS , where St. Thomas Mount and San Thomas Cathedral are located. He was buried in MADRAS. Apostle Thomas established 7½ churches (seven and a half) in KERALA and converted many Brahmins to Christianity.
In Japan, Catholicism was introduced by the Jesuits in the 1500's. Eventually, all of the priests were expelled, and the converts were martyred. When Catholics returned in the 1800's, they found that many Catholics were still there, secretly practicing the faith that they had handed down from generation to generation. There is again, ample historic evidence that this is true.
You can see many excellent pictures of artifacts from this time period on this webpage of an Asian Studies group from St. Olaf who traveled to Japan. Please note, one of the subtitles for a picture says that a statue was used to worship Mary. Remember, this professor teaches about Asia, not Catholic theology!
The museum mentioned on that site used to have a site of its own with many pictures, but it is no longer available. However, you can find another reference to the secret Christians in this description of Oura Catholic Church.
Based on this, I feel that if there were a secret group of Christians which practiced for centuries, there would be physical evidence of their existence.