Adding Cupla affects entire plan

[BB boy]

I had finished the plan (see before snip) then they wanted me to add cupola. I did (see after snips) I followed help article 869, followed to a "T". See before and after snips. Don't know how to fix it. Went back did it over, same thing happens.
After posting, I did go back and try to do the manual roof tool. But after fixing the cupola roof, deleting and manually rebuild the main roof, the cupola only shows roof, no walls