Good question! I talked about decline and eventual end of organized paganism in ancient Egypt in this thread. The short answer is that all overt polytheistic worship and practices had ended by the 6th Century, due in part to the growth of Christianity, and to religious persecution by Christians. Egypt's transition from a culture with many gods to one which only permitted the worship of an Abrahamic god involved violence against both Christians and pagans, as people vied for the right to practice their religion and take control of sacred spaces. The gradual closure of the temples and destruction of religious shrines and sanctuaries - as well as the adoption of Christianity by the Roman state - all helped contribute to this. At the time of the Muslim conquest of Egypt, it was a thoroughly Christian country. However, folk traditions and beliefs persisted within Egyptian communities that had adopted first Christianity, and the Islam. In this way, some elements of ancient spiritual and legendary beliefs outlived their ancient religious framework.

It is an interesting and dramatic story, and one which I hope you will enjoy.