Hi Aaron...
Be careful with the assembly cut out feature. It's very useful... but there are some important caveats when using it. Basically the cut out feature does a simple boolean cut to your airplane surface. While Pro/E can certainly do these boolean cuts, best practice is not to rely on them too much. You're creating external references between the part and assembly. These are not inherently bad... but external references have gotten a very bad reputation over the years due to the potential for them to cause problems. Not effectively managaing and understanding them can lead to circular references (which cause your model NOT to regenerate fully).
Also... those cut out features can begin to slow down model performance. When your assemblies become large and you use either assembly extruded cuts (with auto-intersect turned on) or the cut out feature, regeneration times can skyrocket.
It's great that you found a solution. My advice would be to read up on the cut out feature a little more to understand exactly what price you are paying for boolean-style cuts in your model. This isn't meant to dissuade you from using the features you need... just friendly advice to help you avoid a problem later.
Take care...
-Brian
