The only way is to format the card, I believe. Moving a CF card between any two Canon cameras* seems to retain the card's existing file numbering. If the camera didn't do that then overlapping file names would be possible, either over-writing the existing file or causing an error writing the new one.
* I've tested this theory only with a Powershot S70, Rebel XT, and 5D, but moving a card between any two gives the result you describe.