Did you ask me that before, and did I do some research, and did I forget to get back to you?

I can certainly tell you which file contains the flatten for this, but you really have to think about what you are then going to do. Removing a default flatten for fS2004 is not an ideal solution -- I learnt that when I tried to remove the Wellington flatten, and it messed up Nelson.
I'd be more inclined to just add localised flattens -- around the water edge, and under the airport -- which would be a bit fiddly, but less dangerous.
However, if you are feeling brave, then this is how I'd remove a default flatten:
By the way, the flatten is included in FL994440.bgl in Scenery\Ocen\scenery
I'd use Sbuilder to open this file. (New: Append... LWM Bgl)
Then I'd find the flatten for Whangarei (you can start at Whangarei in FS2004, then use Show Aircraft in Sbuilder to find the flatten.)
I'd then select the Whangarei flatten and delete it. How I'd select all the remaining flattens and compile as a BGL.
Now I'd build a new flatten, and compile that.
To get things in the right place, you then need to disable the default flatten -- by renaming FL994440.bgl to a different extension -- and place your new reworked flatten in Scenery\Ocen\scenery.
The trouble with this method is that the resulting flattens for all the other airports, even though they appear to retain their proper elevations, sometimes don't work as expected in FS. This means that you end up with a change in elevation. Maybe another tool would do a better job, but I haven't looked for one.
You also need to somehow disable the default flatten as part of your installer.
Disabling in FSX is a lot easier -- you simply 'cross out' the flatten with an exclude BGL, then build a replacement -- no messing around with default files, and everything can just be distributed in your normal scenery folder.