If you have a topography and use a building pad in Phase 2, it will cut it in Phase 1 as well. Autodesk has aware of the problem since at least 2011 and has acknowledged that the feature is not working as it should.

Right now the work around is to create a whole new topography in Phase 1 to cover all the hole. This leaves a mark that cannot be hidden in some case (when using Realistic views with grass materials or view a 3d view for example). Mostly, this workflow should work as expected. Adding a phase 2 pad should only cut the topography in phase 2 and not create a hole in the topography in phase 1.
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I would suggest revisiting the way topography works with some experienced Landscape architects. The landscaping workflow is one of the weak point of Revit and it seems to be getting very little attention. For example, I would suggest some elements that are capable of "eating into" the topography, so for example if you add pavers to a topo, you don't have to push the topo down manually.
I would also suggest giving us access to editing the edge of the topo instead of giving us only the clumsy "split" and "merge" surface tools.