I backed up my SP's CF card onto my computer making sure to copy it rather than cut it and since I've put the card back into the SP when I got to one of banks C-J it flashes up saying FNT like I'm trying to format it. The computer still reads the card so I hope it isn't the SP's card reader that is the problem I've looked at that and there are no bent pins. Any ideas anyone?

Were you able to fully copy it to your computer? If so, format it on your computer, then format again on the 404. Then manually bring your samples and patterns back in to the cf card with the Roland software.