sporadic results when using penetrations (resetting elements, etc.)

 Good afternoon all,

we have went through an exercise of creating a "voids model" for the MEP services which we are merging into our architectural models to cut the penetrations. The results are mixed - some items cut perfectly, some cut half way through, and some seem to reset existing voids and/or instance data. See attached for example.

Does anyone know what might cause this behaviour? Ideally we want to just select all -> copy through so that all walls are cut, but this isn't a good method as its not until later that we find where it has caused us issues.