There should be no problem switching cards between bodies after formating them on the body they will be used on. I do it all the time. The camera should remember the numbering sequence it has been using (in continuous numbering mode).
However there are always problems if you shoot with multiple cameras. Whatever numbering mode you use you can generate duplicate file names if you are using two cameras, whether or not you swap memory cards. The solution is batch file renaming when you transfer the files to your hard drive.
Here's what Canon say:
Continuous numbering, as the name suggests, numbers each new image in sequence from 0001 to 9999.
If you remove one CompactFlash card and replace it with another newly formatted card, the sequence will continue.
The advantage of this system is that, until you reach image 9999, every file will have a unique number. This can help avoid problems when you download the images to a folder on your computer, but it might not be ideal for your set-up.
For instance, if you use two EOS non-pro digital cameras, you will obtain matching file names. The safest way to deal with this is by batch renaming.
Auto reset returns you to the start of the number sequence (100 for the folder, 0001 for the file) each time you insert a newly formatted card into the camera. Here, though, you will get duplicate file names every time you change cards. Again, the solution is batch renaming.
If the CompactFlash card you insert into the camera already contains image files, the numbering sequence in both continuous and auto reset modes will continue from the highest file number on the card, rather than continuing the camera sequence.
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