Granted that linguistics doesn't account for everything, but it simply can't be completely dismissed in such a cavalier manner without so much as a reasoned, fact-based and historically sequential explanation.
There is also the fact that genetic studies pertaining to modern Nubians explicitly conclude that "an
unadmixed’ Nubian gene-pool is genetically similar to Nilotes"...
..And that the admixture event for the modern Nubian population took place 750 years ago. It doesn't matter where the modern Nubae-Nobatae (Nubians) fit in genetically today. I don't much care for that.
The citation is in this source:
Author summary Northeast Africa has geographic and historical links to Eurasia via the Middle East and the Arabian Peninsula, but the demographic history of the region itself has been more elusive. We investigate genomic diversity of northeast African populations and found a clear bimodal...
journals.plos.org
Explain relevance of a certain "Cushitic" tribe residing with the Nubians in the last couple of centuries and subsequently adopting a completely unrelated language, apparently relates to the origins of the Nubians.
You're on a run with this irrelevant point.
Please explain the relevance of an Arabized Nubian tribe having clans that reside with the Beja and adopting a completely unrelated language -- in a different phylum.
There is no link between the Nubian language and the Beja language. It's beyond irrelevant if the two groups have intermixed recently.
It's not a "conspiracy theory" that the Nubae-Nobatae migrated to Upper Egypt per the invitation of Diocletian; it transpired in the light of history and there is ample evidence to affirm it.
Nubian language origins:
Source from Cambridge:
The Languages of the northern sudan: an Historical perspective - Volume 7 Issue 1
www.cambridge.org
You have completely failed to provide even so much as an iota of evidence that the Nubae-Nobatae somehow went extinct.
The onus is on you to prove that the Nubae-Nobatae people (and their medieval Christian kingdoms) somehow became extinct even though historians recognise them as the Nubians of the medieval period.
The Nubians, Nara and tribes in Darfur are part of a Central Saharan complex; take away the recent Arab introgression, and it becomes clear that the Nubians were genetically similar to these Central Saharans. It's no coincidence that the Nubian language is closest to another Nilo-Saharan language -- Nara.
Central Saharans have E1b1b lineages as well as A-M13 Nilotic markers because these populations are composites of proto-Nilotics and E-M215/E-M35 populations.