I just bought a used MK3 and set the recording up to separate cards .. RAW to the main CF, and JPEG L to the backup SD card.
So what I do is download the files from the CF card to my computer, then put the CF card back into the camera, erase all files & format the card. But when I shoot again all the old backup files on the SD card are transferred to the CF card.
For example if I do a shoot of 1,000 files then download those files from the CF, erase the files from the CF, format the CF, then do a second shoot of 50 files when I download the second shoot there are suddenly 1,050 files on the CF card .. not good. So somehow existing files are being transferred from the SD to the CF. I can stop this by formatting the SD after every CF card change but I don't want to do that because I sometimes still need to have the backup files on SD.
I have my MK2N set up for recording exactly the same way and it just records new shots on the CF as they are taken, and does not transfer old files from the SD card every time I put a new CF card in.
I must be doing something wrong with the folders or setup but I don't know what .. help!