No, the directory structures would exist in parallel (we're assuming here that both the Canon & Nikon have similarly compliant filesystems - ie. both working to the same spec) - worst that would happen in that case would be that you would have one directory tree for the images taken in the Canon and another for the Nikon (at least that's how it works when moving a card between my Sony Cybershot, EOS & HTC phone - one directory tree for each)
In this case most likely faults: Something to do with the write protect on the SD card or something to do with the assembly that reads the status of the write protect in the camera (could be dust/similar). Obvious test - try another SD card... not expensive even if you don't have one lying around the house, and not a bad thing to own a spare so if one corrupts while you're out you're not in the situation of "take no more pictures" or "format the card and lose all the pictures you took up to now" - spare card allows you to keep shooting and worry about recovering the first card when you get home.
