Which Directory Opus version should I use

If you have a licence for Opus 12 then there's no reason not to install the latest version.

Don't copy the program folder from the old machine/HDD; it won't do anything useful and could mess up the file permissions. Just use the installer on the new one.

If you want to copy your configuration from the old machine/HDD to the new one, the way to locate it is explained here: How to backup or locate your Opus configuration (Simple)