It's important to learn the new-to-you Archicad terminology.
If you used Solid Element Operations (SEO) as you first mention, then you have established a relationship between the roof and wall in question. Changing one and/or the other does not change that their is a relationship and the wall will adjust to the roof changes. For example if you change the angle or height of the roof, the wall will still be trimmed by the roof but at the new angle or height.
If however you used cropping as you mentioned at the end, then you do need to establish a new relationship between the two as Eduardo described.
Erika
Architect, Consultant
MacBook Pro Retina, 15-inch Yosemite 2.8 GHz Intel Core i7 16 GB 1600 MHz DDR3
Mac OSX 10.11.1
AC5-18
Onuma System
"Implementing Successful Building Information Modeling"