Hello Linz,
recently I have increased basement height in Project too, using Story Settings Dialog & that wasn't difficult. I describe you how do I do that.
In story stettings dialog I set new Elevation of Basement Story (in my case is #-1) & "Height to Next". Then remodify heights of all Walls, Columns, Beams Elevation(s), etc, except of Floor Slabs, using Find&Select Dialog.
Example:
Before:
# Name Elevation Height To Next
-1 Basement -3.3 3.3
After:
-1 Basement -4.3 4.3