A collegue used copy design to create a new assembly from an existing assembly that I had in vault. After the operation completed it gave my origional assembly a new version and relinked all part with derived components from the original assembly to parts in the new assembly. This should never happen. I need help quick. We use copy design quite often and have no Idea how many other assemblies are screwed up due to this behavior.
In the attached pics. The origional assembly had all links to files with the number 36810 in them, you will see they now reference parts that have 36927 in the name which is the new assembly that was created using copy design.
I also had same problem, But after that we changed our CAD modelling process.
As per my knowledge, your model some parts are changing but some are common for both and those are created from same base component. This common base component creating problem in your case.
You need to create common parts and variable parts from different base components.