I was a little confused with what your problem was but what you are saying is the bevelled edge (skirting) at the bottom of the wall is being cut off when you connect (trim) to the roof above.
This is because when you connect elements to a roof then anything outside of the roof cutting body will be removed.
The roof cutting body has two positions - contours down (i.e. matches the outside plan perimeter of your roof) or pivot lines down (matches the pivot line position.
You can turn the trimming body on/off - VIEW menu > On screen Options > Trimming Body.
So in this case you either need to extend the perimeter of your roof (which you probably don't want to do) or adjust the pivot line position (which again you probably don't want to do).
So all you are left with is using Solid Element Operations with upwards extrusion as you mentioned.
This should only cut the walls off that extend above the roof.
I am not quite sure why your entire wall is being cut away.
Barry.
One of the forum moderators.
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