This hasn't been my experience with the S95 and 60D.
When swapping cards between the two, the 60D started a different folder and preserved it's numbering.
I thought it was a bit annoying, so I haven't done it since then. Like others say, I format my cards in-camera (low level) usually once per big download session. My experience has been that formatting helps with write speed . . . but that's anecdotal, not scientific.