Problem Importing Topics Between Projects

This has fast become my new favorite place!

Ok, here's the scoop:

We had RoboHelp x5 and just moved to RoboHelp 8 a month or so ago. Shortly after the conversion, we copied all of our topics from our original project into a new project for a new product we're rolling out later this year.  The products are similar, but the names of screens and windows are different, so when a new topic is created, slightly different versions need to be created for each. I thought instead of manually changing each topic I could create the topic in one project, then open the other project, import it, and change the template to match the color scheme for the other product and be done with it.

But somehow my doing this caused almost all of the nearly 3000 topics to become "not controlled" in RoboSource Control, affecting myself and 5 other developers. What about the import would cause this to happen and is there a way to prevent this?

I was hoping that for each change we could just change one, import to the other and call it a day instead of having to manually do it twice. Is there a secret way of doing this that doesn't break the system and irritate my co-workers?

Thanks,

WD