If I add to the existing Fort Sungard, with an additional tower and a door to a new player house, when the enemies reset and the associated questlines come around, will my addition and minor changes be affected?

I know the flags will change out and a different set of enemies will take over. I thought it would be interesting to set up shop there and place some Follower/Guards at the addition. When it reset with a new faction, they would go at it in defense of the takeover.

However, I didn't know how or if this would affect anything. My group will all be Vampire Faction so any respawns will be hostile.