The next Pharao wanted to erase all traces of his father, and ordered the destruction of a lot of the documentation regarding his reign, including a lot of inscriptions and monuments.

He also prohibited the worship of most of the Egyptian pantheon, declared that he was the only one who was allowed to pray to the remaining one. Basically, he grabbed a lot of power from the priests. That, of course, also resulted in some destroyed religious texts.

Furthermore, many of the more mundane texts were on clay tablets that were occasionally wiped and re-used.