ZizZax the Almost Wise was 'almost' wise because he can not teleport or (IIRC) open rifts between different realms. Dragons had many places they could have gone, in or out of the world of Rivellon. Of course, dragon knights were created as intermediaries in the first place because dragons were reclusive, so any even remotely as powerful as Patriarch could simply stay where they were (possibly helping dragon knights to leave or hiding them).
The Divine banished Damian to the world of Nemisis, populated by the Raanaar, a race who could open rifts between realms. In his attempts to return to Rivellon (described in the novella and backstory throughout Beyond Divinity), Damian built up a fair Black Ring presence there, and forged alliances with various demons, etc. It is possible some dragons and dragon knights moved there to continue the war with the Black Ring (or were there and stayed), when the humans in Rivellon diverted their attention to dragonkind.
