EDIT: APRIL FOOLS! There is no connection between Egypt and the Khoi, Atenists did not influence Zoroastrianism, and they definitely didn't go to Laputa (a flying island in Gulliver's Travels). I'm going to put together a take-down post and comment it here.

After Tutankhamen (well, more Ay, the regent) restored the old Egyptian religion, Atenism became very unfashionable and Atenists found themselves in a very politically (and physically) dangerous position. Staying in Egypt was no longer safe- but where to go?

Though there weren’t any records of what happened to Atenists, their presence post-Akhenaten in a surprisingly varied number of places is evident. An Atenist community thrived in what is now Iran; centuries of syncretism between Atenism and Indo-Aryan religion eventually produced Zoroastrianism. Laputanists have recently begun to appreciate the influence of Amarna artists on the iconography of in early Lagado palace complexes. However, it seems that one group of them in particular went to a far off place indeed.

Wilhelm Bleek was one of the first people to study the Khoi languages in depth in the nineteenth century. The Khoi/Khoe people are native southern Africans who are quite similar to the San, or Bushmen. However, unlike the majority of San groups, they were (and some still are) nomadic pastoralists who depend on cattle and sheep. Furthermore, their languages, though still filled with clicks, are quite different from San languages. They’re fairly fusional and have grammatical gender, absent in San languages but present in Afro-Asiatic languages- including Egyptian. Bleek was familiar with Coptic- the modern descendent of ancient Egyptian- and recognized that Khoi was quite similar. A few decades later, Thatch sealed the connection and it’s been accepted ever since.

This all fits in with archaeological and oral history evidence pointing to the Khoe migrating from the North around 2000 years ago. Recent genetic studies have shown that Khoe have a small but detectable bit of Near Eastern ancestry fitting with the Coptic connection. Henri Breuil, a pioneering expert on rock art, independently recognized Egyptian styling and motifs in southern African Khoe art. Even more clues lie in Khoe religion. The Khoe are monotheistic, with a single god and his earthly counterpart. The earthly counterpart’s main feature is his continued death and rebirth- a very Egyptian idea, and one that fits in with the divine self-image Akhenaten meant to cultivate.

All the evidence points to a small group of Atenists migrating south, mixing heavily with the native people, and forming a new hybrid culture. It’s quite a long migration, but not without precedent- after all, Lagado is thousands of miles from Egypt!

Sources

Thatch, M. Inflectional Morphology Supports Coptic-Hottentot Connection.

Barnard, A. Hunters and Herders of Southern Africa: A comparative ethnography of the Khoisan peoples.

Bernal, M. Black Athena: The Afroasiatic Roots of Classical Civilization, Volume III: The Linguistic Evidence.