Thanks for your answer Ashley,
I installed the latest beta release r238 and exported my project with cordova. In the options I enabled "Use new Intel XDK project format".
After I loaded the .xdk file in the Intel XDK, configured all my build settings and imported the icons and splash screens, I get the same error as before. The files that can't be found (icons and splash screens) are in the right folder though and I can even open them in the built in file explorer in the Intel XDK.
I'm not sure if this still is a compatability issue between XDK and C2's new project format or something else.
I just tried disabling the "Use new Intel XDK format" option but I got the same error again when trying to build (It fails while uploading the project files).
So it seems like it doesn't have anything to do with C2 I think. I'll probably have to wait until the next XDK release and see if it works then.