The answer to this question is very simple.........the Medieval Arab Muslim conquest.
It is true that in the early middle ages, North Africa-(from Egypt, to Tunisia), had a sizable Christian presence-(both Roman and Byzantine rite). In fact, much of North Africa, during the early Middle Ages/(the so-called, "Dark Ages"), was under direct Byzantine imperial rule. The famed early Medieval Roman rite Christian, Saint Augustine, was probably of Berber ethnic extraction and was originally from either Libya or Tunisia. One can even go back to Saint Mark, who was also from Libya and is the Patron Saint of Egyptian Coptic Christianity.
However, with the birth of Islam in the early 600's, followed by the subsequently rapid spread of Islam throughout the Arabian peninsula, as well as throughout the Middle East, neighboring North Africa would shortly follow....... from Egypt,to Morocco. The North African Muslim campaigns were led by the Umayyad Caliphate and many-(though not all) of North African's Christians, were forcibly converted to Islam. Egypt, for example, is approximately 15% Christian, though the presence of Christians in the remainder of North Africa is infinitesimal.