There was never any real war against Avernum by Vahnatai or a clan as a whole.
After Avernum 2, a group of Vahnatai left the Olgai clan to follow Rentar-Ihrno and exact their revenge against the Empire. They were considered rogue Vahnatai. {*AVERNUM 4 SPOILERS*} (highlight text to read)<font color = white> After Rentar-Ihrno's defeat, an even smaller group of Vahnatai led by Rentar led an attack on Avernum's people and cities but were defeated. They were opposed by most of the Olgai clan. </font>{/SPOILERS}
As for using the same NPCs as in VoDT, I don't think that's really a good idea, especially if you're setting your scenario in Avernum. They can be from the same clan, which would make sense for them not to really know about Avernum or previous encounters of Avernites with Vahnatai.
Vahnatai have a large sense of honor, but more important to (most of) them is wisdom. There was infuriating inaction from the majority of the Olgai clan which led to Rentar-Ihrno splitting off in the first place. I would suggest emphasizing the sacred nature of Crystal Souls and the unfathomable intentional destruction of one rather than an 'honor feud'.