Ok, so I've been shooting on my Canon 7D for over four years, and prior to that, shooting timelapse sequences on my 350D since 2004.
I wanted more from the image quality and decided to buy a Canon 5D, and hack it with Magic Lantern. It doesn't compress the image, and essentially you end up with a sequence of RAW stills. This requires super fast CF-cards, and they need to be huge (I've got 4x128GB).
The problem is now, that some clips are exceed the 4.29 GB limit on a FAT 32 formatted card. (I should have formatted the card in another limitless format) - so the RAW image sequence are now corrupt.
I found a programme though called Hex Fiend that can open the code of the corrupt RAW file. As far as I understand, the programme needs to know where the files begins and ends.. and by adding this code you can "Save the file, and start unpacking your DNG's!"
Nice to know that I can, if needed salvage some of the footage. I use RAWMagic Lite to create .DNG's. DNG's are basically the standard RAW format, across different manufacturers, as implied by its meaning - Digital Negative. From this, the grading opportunities and sharpening possibilities are just immensely better than a plain JPEG or H264 video.
The Magic Lantern forum has been of great help with this issue, and also this guy's clear guide
To avoid the 4GB limit issue (corrupting files) in the future, I will format my CF-cards in ExFAT. Easy howto guide for Mac/iOS here.