This is a tricky area & requires some pre- thought when placing cross sections.

You make the window cut outs ('holes' as you call them..)  by removing points on a cross section but bare in mind when you do this you will loose the ability to manipulate cross sections - --  
So you need to make/insert the cross sections - & position them & be perfectly happy with the shape & position of points before you start to remove those points.

The secret is to backup your project with new filenames whenever you make a major change - for instance b7e7_1.fsc, b7e7_2.fsc, etc...

That way when you make a big oops - you can go back to the stage before you went wrong.

Another important thing is to make a copy of the section before you remove the points so you can use this as your glass. The way to do this is to select all the points where your window will be - copy & paste & rename this new part as 'glass_1.fsc' or similar. You can make this transparent & reflective later.