And remember, politics back then were not much different. The empire was basically a familial based oligarchy, with competing family groups gaining control of the empire over the centuries.
It was not unusual at all when an overthrow took place to try to eradicate all evidence of preceding reigns.
There were over 700,000 texts lost when Alexandria burned.
We don't know yet what lies buried in the Vatican.
When they finally publish the Dead Sea scrolls, we might find out.
In a work issued in 1959, Father Kirschbaum, a member of the archeological commission excavating under the basilica during the 1940's, has given a summary of the findings. These are in brief that it is reasonably certain that the place where St. Peter was buried has been discovered. According to historical records, supplemented by these new discoveries, this is the "history" of the tomb. The Christians buried the Apostle's body in a simple grave on the southern slope of Vatican Hill and covered it with a few brick slabs. Soon other graves were made near that of St. Peter, and these have been recently discovered. Their existence and inscriptions on the wall make clear that from the very first St. Peter's tomb was a place of pilgrimage so that there was uninterrupted Christian veneration and observation of this spot.About the middle of the second century the grave was marked by a simple monumental slab, the "trophy" mentioned by Father Gaius about 200. During Valerian's persecution, when Christian cemeteries were closed for the first time, St. Peter's relics, but probably only the skull, were moved to a more secure place on the Via Appia. They were returned in the fourth century when Constantine began the first basilica over St. Peter's tomb. To this end he went to great labor and expense to fill up piles on the sloping Vatican Hill to provide a level foundation. This is why St. Peter's tomb is at a considerably lower level than the floor of the Basilica of Constantine and its modern replacement.
St. Gregory the Great carried out extensive alterations between 594 and 604, placing an altar over the tomb, but leaving a shaft through which objects might be lowered to touch the tomb for the veneration of pilgrims. During a Saracen raid in 846 much of the basilica and tomb were plundered, although the actual grave was not penetrated. It was soon after, probably, that the skull was removed and placed, together with that of St. Paul, in the Lateran, where they still remain. To prevent further vandalism the tomb shaft was filled up and the crypt sealed.
In 1503, work was begun to construct the modern basilica which was built over the tomb without disturbing it. During construction some attempts were made to reach the tomb, but were abandoned, it is now clear, before reaching the actual grave. The discoveries of 1940-51, however, successively penetrated the various layers and reached the actual site of the original grave of St. Peter. Here were found bones, all belonging to the same person, "an elderly and vigorous man," with the skull missing.
The cautious archeologists will affirm no more than that these bones were believed to have been those of St. Peter by those who detached the skull for preservation during Valerian's persecution in the third century. In view of the continuous record up to that time of Christian devotion to the tomb, we believe that this ought to be enough to satisfy any reasonable man.
We may conclude, then, that not only St. Peter's authority and spirit, but even the relics of his body, have remained in Rome. Nature and grace have conspired to justify the Latin inscription on the dome of St. Peter's Basilica, towering some 400 feet above the once simple earthen grave: "You are Peter, and on this rock I will build my church, and I will give you the keys of heaven."