When I took some photos with my D7100, I noticed the file sequence number and the shutter count didn't match. Thanks to @nickt for a link that explained the process, I was able to match them up.
In the shooting menu of the D7100 (and no doubt a menu option for other bodies), d7 gave me the option to change the first 3 letters for the file name. Below that is an option to reset the file sequence number to 0000. The option to reset the file number was staring me in the face, but I didn't see it until Nick told me to reset the digits there (even Jake said the option was there but I just hadn't seen it).
After pressing the option to reset the digits, I had to go through a short process to change the actual file number sequence to match the serial number. So I took one photo which gave me the file number of 0001. I inserted the memory card into a card reader on my computer and uploaded the image to CameraShutterCount.com to obtain the shutter count.
Then I went back to the memory card which was still in my computer's card reader and changed the file digits to the same 4 digits of the shutter count. When I was finished, I did the same thing for the second card and inserted both cards back into their respective slots in my D7100 (first slot shoots NEF and second slot shoots jpeg) without yet reformatting the cards.
I took a few additional test shots and saw on the back of the display the file numbers were shooting with the next digits in the sequence. And to be sure, I pulled the cards out and checked the shutter count. I reformatted both cards in camera and took a few more test shots. The numbers definitely continue in the correct sequence.
So if your shutter count doesn't match your file sequence number (and if you want to change it), this process should allow you to reset it correctly.
In the shooting menu of the D7100 (and no doubt a menu option for other bodies), d7 gave me the option to change the first 3 letters for the file name. Below that is an option to reset the file sequence number to 0000. The option to reset the file number was staring me in the face, but I didn't see it until Nick told me to reset the digits there (even Jake said the option was there but I just hadn't seen it).
After pressing the option to reset the digits, I had to go through a short process to change the actual file number sequence to match the serial number. So I took one photo which gave me the file number of 0001. I inserted the memory card into a card reader on my computer and uploaded the image to CameraShutterCount.com to obtain the shutter count.
Then I went back to the memory card which was still in my computer's card reader and changed the file digits to the same 4 digits of the shutter count. When I was finished, I did the same thing for the second card and inserted both cards back into their respective slots in my D7100 (first slot shoots NEF and second slot shoots jpeg) without yet reformatting the cards.
I took a few additional test shots and saw on the back of the display the file numbers were shooting with the next digits in the sequence. And to be sure, I pulled the cards out and checked the shutter count. I reformatted both cards in camera and took a few more test shots. The numbers definitely continue in the correct sequence.
So if your shutter count doesn't match your file sequence number (and if you want to change it), this process should allow you to reset it correctly.