I also asked Canon the same question and first off they said
"This is normal. The file numbering system will be indicative of the amount of shots taken on the card."
So thinking they had missed the point I referred them back to my original query and they responded
"When the camera is set to Continuous Shooting, it checks the file numbers on the card and gives the next shot the next number.
If the card has been used in a different camera, then file numbers may have been written in a different way to your own, but your camera would then write the next file with a number following on from the last one on the card.
As there are only 2 different ways of setting the file numbering on the camera, Continuous and Auto Reset, it is not possible to set a the numbering on the camera. "
So I think the long & the short of it is we either continue from where we are or go back to 1 but there is nothing in between
