I finally got around to borrowing Bechhaus-Gerst's Sprachwandel durch Sprachkontakt am Beispiel des Nubischen in Niltal. It's tough going because I don't really speak German, but she briefly suggests (p. 37) that the C-Group Culture of 2200 BC-1500 BC in lower Nubia, known as Temehu to the Egyptians, were Berbers (referencing Behrens 1984/5), and that Nobiin-speaking Nubians came in about 1500 BC and replaced them. This would explain the possible Berber loanwords in Nobiin, notably aman "water". Apparently, the archeology shows a change of cultures and of body types around 1500 BC, and ancient Egyptian paintings first begin depicting their southern neighbours as black around this period, while the Egyptian loanwords in Nobiin seem to date to the New Kingdom or later.
The identification of the Temehu with the Berbers is not based on linguistic evidence, as far as I know, and the small inventory of possible Berber loans in Nubian is neither conclusively established nor necessarily dates from as early as 1500 BC. So I don't know how much confidence to put in this scenario. However, it points to an interesting avenue for studies of Berber to explore. A lot of evidence suggests that Afroasiatic originated further east than North Africa, so it would make sense for there to have been Berber speakers in the Nile Valley - that could even be where Berber spread from in the first place. I previously discussed this issue in The Berbers of Southern Egypt.
The book is interesting for other reasons, incidentally - if her scenario for the development of Kenzi/Dongolawi is correct, it has borrowed an astonishing amount of grammatical material from Nobiin.
Behrens, P. 1984/5. "Wanderungsbewegungen und Sprache der frühen saharanischen Viehzüchter", SUGIA 6:135-216.