I was recently trying to upload a video to YouTube but kept getting the Rejected (duplicate upload) message.
I found the easiest way to get around this is to change the metadata on the video you are trying to upload. In my case it was an mp4 video.
To change the metadata I used a program called AtomicParley:
After downloading it simply run
AtomicParsley.exe "example.mp4" --artist "Me"
Or whatever artist you want. The new file will be written out with new metadata. This should then pass any YouTube duplicate content check.