Moving this discussion to the Premiere Pro forum.
Are you speaking of the Canon 1D-C? If so, I had good luck with the following workflow:
First, I used the EOS Movie Utility for the 1D-C to "stitch" together files into the original "broken" takes. Double the media but c'est la vie!
Next, I used Mpeg Streamclip to transcode the motion jpeg files into 422 Prores files at the same size. Those files imported beautifully and play well inside of Premiere.
Brilliant! I'll give that a go!