I don't think there is much doubt in the accuracy of the versions of the New Testament books we have today compared to their original editions. The main contentions are over the authorship and their history. The Epistle to the Hebrews was attributed to Paul, but this was called into question even when it was being selected for inclusion in the canonical list. Half of the other Pauline epistles are considered by many modern scholars to be fake.

There are known to be other gospels and epistles that were in circulation in the second and third centuries, and the oldest surviving manuscript of the Gospel of Thomas is roughly contemporaneous with the oldest surviving of the canonical gospels. So why is the Gospel of Luke more authoritative than the Gospel of Thomas? The short answer is those who the modern Christian churches choose to believe are authoritative found one more in agreement with it than the other (note that this does not pass judgement on whether or not that belief is historically accurate).