Converting From A Custom Post Theme

I have a friend that wants to convert to Atahualpa after using a very restrictive theme. The only catch is that the theme has a bunch of Custom Post templates.

What will happen to the existing Custom Posts if I just activate Atahualpa? Will they be preserved into default format? And if so, what happens to the Custom Field content?

Is there a clean way to preserve the Custom Post types? I'm assuming I have to make new templates. Do I just have to duplicate the Custom Fields into the new templates?

Thanks!