Okay, never mind, I found a post detailing what to do. For others that stumble across this:

1. Open SH3D
2. Click 'Help' on toolbar
3. Select 'About'
4. Click on 'Libraries'
5. Double-click on the library you want to remove, this will take you to the AppData folder where it is at
6. Delete the library
7. Close and restart SH3D
8. Done =)