I've never seen a faction re-emergence in RTW, but maybe it has to do with the brigand bands that are led by "named" generals. I've never seen these groups early on in the game, but I did tend to run into them quite a bit later on in my Jullii campaign after a number of factions had been destroyed.

Only 2 problems with this.
1. These groups are usually as intimidating as a regular brigand army- I could'nt see them being able to take a city over.
2. I don't remember any faction-specific units in these groups.