I've been having the same problem.

I use "Open For Edit" on a resource, copy it into my mod's package and link it to a script. Even so, the original resource isn't marked as innactive and the script can't be built (it says it isn't linked to any resource). Futhermore, when I reload the project, the copied resource is gone...

I also want to know if there is a way to replace the core scripts, because all I wanted to do was include one charScript to Base or DefaultCharacter so all characters would have my script attached to them.