We are talking about 'Present Time' here so roughly 4E 201.
Personally I think that the obvious would happen. The Nerevarine would either look for Dunmer refugees in the Telvanni lands or go to Solstheim. Regardless of where he goes he will unite the Dwemer there using his speechcraft and wage war against the Argonians.
He will absolutely crush the argonians using some fancy Akavari war-techniques and rebuilt Morrowind social structure with him as the sole and absolute leader.
This conflict that will be known as the salvation war or something by the argonians but will be called The Slave Rebellion or something by the Dunmer will also somehow see the return of Vivec. Vivec would be slain by the Nerevarine because of some mysterious reason the Nerevarine learned by travelling to Akavir and meeting the continent's inhabitants.
What do you think?