How to work with entresols / mezzanine floors in lofts?

[gold333]

I'm working on a 4 story house in Amsterdam. The second floor has a section removed (marked in green) to allow two mezzanine floors to be built. This is because street level (purple) is 3 feet higher than the floor of the ground floor.

However, when I model all the floors in CA and use Build->Floor->Hole in Floor, it leaves this residual edge of the outline of where that section of the 2nd floor was, that's preventing me from installing normal sized doors and windows for the entrance.

How can I get rid of the green outlined structure above the entrance door and windows in the last picture?

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