Hey, Lindsey,
I have also encountered difficulty with broken C300 file structures and spanned clips. It’s possible to bring them in as their separate components, but that’s a big drag.
The workaround I have used successfully is to go to an older project with an intact CONTENTS and CLIPS001 folder. I copy those folders onto a new drive, delete their contents, and use them as a template file structure for the new project. It doesn’t work if I just create a new folder called CONTENTS, but if I borrow it from something previously created by Canon it seems to work out just fine.
Hope this is helpful.
Peace & respect,
Joy E. Reed
http://www.ohmyproductions.net