I ran into this problem while travelling. I wandered into a camera shop, and asked to try out a Canon 5D they had on display. I took the CF card from my 40D, put it in the 5D, fired off some shots, and then put the card back in my 40D. I quickly viewed the photos – the 40D had no problem displaying the 5D’s images, but the file numbers had changed. I didn’t notice this immediately – only that evening when reviewing the day’s pictures. The 40D was on 5000 odd, and now, all of a sudden, it was counting in the 8000 range.
I realised that this was because the 5D were on that many shots, and my 40D is set to “continuous” – it simply continued where the card stopped. While this makes no difference to the operation of the camera, the continuous file numbering is the only way I have to know how many clicks my shutter has done. So I wanted to fix it. Since I was travelling I didn’t have the tools at hand to make screenshots, etc, so I did this again on purpose, just on a smaller scale. Here’s how to fix it: