That we churchmen hid a bunch of texts we didn't like is an old trope. Secret Mark contains a different ending than ordinary Mark—but neither ending is original. Moreover, there was no central library where Christians of antiquity could go to catch up on all the variants. (And no, Christians did not burn down any libraries.) So several versions are to be expected.
The word "begotten" is agennetos, and the Father is often called the agenetos—one less "n". The root is genao, "to generate". "Only-begotten" in John 1: 17, monogenes, means "one of a kind", "only one of a set of one". The reality bursts the bonds of human language, of course.
Finally, the Dead Sea scrolls are fascinating, and not threatening to Christianity. They put paid to the idea that the original texts were copied so many times that they are unreliable, for instance.
There are and always have been people for whom Christianity was a path to getting power and keeping it. They are of course allergic to any idea that threatens their stunted version of the Faith.