I wonder if it would be possible to remove windows, doors and prefarable curtainwalls from walls and slabs without leaving holes? In many cases I have IfcOpeningElements.
For the most part it should delete the IfcOpeningElement with the window /door/ curtain wall,
if it does not delete them then you can regenerate the wall with shift+g (with the Bim tool selected)
is it possible to share an example of the problem you are having?