Hi Dean.
Unfortunately I didn’t find a way to recover the files and we lost the shoot. I tried nearly all the data video recovery apps i could find online, data recovery specialists and had quite a lengthy consultation with the Cannon desk themselves. My files seemed to be corrupt beyond repair and I had to stop trying to find a solution as every day I spent trying to fix the shoot meant that it cost us more money on what seemed a lost cause.
However I think I found the culprit, and in my case I am pretty sure that it wasn’t the camera that was at fault, but the FW 800 card reader we were using to backup the files. The problem only started when we bought the reader and I managed to recover some cards that displayed similar symptoms using a different reader. Although weirdly the faulty reader even managed to write corruption onto the cards themselves and ruin some individual clips actually on the source media.
The card reader in question was Delock Card Reader-FireWire 800 CF extern, any chance you have the same piece of kit?
Sorry I couldn’t be of more assistance. I hope that you have a better resolution than I did. If you do find a way to recover the files please let me know on here.
Good luck!