I have an assembly that is made up of another assembly and some parts. I want to remove a set screw that is part of the assembly within this assembly without affecting the original assembly. This seems like it would be easy, but everything I try keeps messing up all the originals and not just affecting the current top level assembly I am working on. 

So, how do you do this? I have even tried making configurations of the sub assembly and then that just messes up the assemblies at a lower level also. 

We are buying a gear that has a set screw in it. I then make an assembly of this gear and drill and tap some extra holes which makes it a custom part. I then use this custom part in another assembly and that is where I need to remove the set screw that is included with the original purchased part. I want to it to show in the purchased part (also an assembly drawing since it is a gear and a set screw), and the custom part, but not once I get to this higher level assembly. 

It could be used for something else later where this set screw is needed, so I do not want to remove it until I need to.