Fortunately, this didn't happen on a paying shoot, so I have learnt a valuable lesson without too many consequences.
I own a Canon 600D and a 550D. They both have Magic Lantern installed on their respective cards. We were shooting something last night using the 600 as a b-cam alongside my Ex3 as the a-cam.
We were getting a bit low on space on the 600, so I got out the 550 to swap it with. Then my cam op had the genius idea of rather than the hassle of switching the cameras on the tripod, just swap the cards instead. 'Oh yeah, great idea!' I said. So we did. Forgetting that Magic Lantern for the 600 is slightly different to Magic Lantern for the 550.
The card seemed to work fine with no warnings. Watching the footage back today though and oh dear. The file sizes are tiny - measuring MBs where they should be GBs. The frame size is right - 1920x1080, but the picture is blocky and pixellated and just looks like it's been badly compressed.
I don't know why the ML firmware hack should be different for the two cameras but they are and there's obviously a reason. I'm slightly annoyed that no warning came up when we used the 'wrong' card, but I can't blame ML or anyone else for my mistake.
Alls I know is that if you own 2 different model Canons and you're running Magic Lantern: THE CARDS AIN'T INTERCHANGEABLE!!
Ok, this is quite embarrassing to admit, but it seems that user error was the cause of the issue, not hot-swapping the cards.
According to the ML user group on Vimeo, the latest version of ML has all models bootable from one card - the camera detects which is the correct one to use.
What happened to us was, that after swapping cards we managed to somehow knock the bitrate down to 0.1. We should have been at 1.0. As such, the resulting footage has about 10% of the quality it should have.
So the lesson here is not that ML cards aren't interchangeable, it's check your settings and check em again.
And perhaps don't post on forums before checking all possibilities...