While in the process of moving some packages with the script, I'm wondering what is going to happen when one of them is to be updated by the application manager (or apt-get).

It is going to install its new files in their pristine position, on the root filesystem, overwriting the links, and leaving parts of the old packages on /opt? Shall it get me into trouble? What am I going to do with those remnants on /opt?

Or I better undo optification of packages before I update the packages?

Thanks for your responses.