It is not the shutter counter that is mixed up, it is the file counter.
Your shutter counter you can not reset.
Go into your camera menu (mine is set to Dutch, so I'm not sure abuot the name
), but go to the third top level tab (the one with the tool symbol), select the "File Name" option, move the cursor to the right here. Now select "Reset File Name".
This will reset the file counter the next time you put in a memory card with no previous files into your camera.
If you do not have any other SD cards, first copy all files to a computer and format the card, then reset the file counter.