I never delete a characters 9000,0, 9000,1, & 9,000,2 portraits, My way of doing it is open your character with Fighters factory then save the character as 1.1 before making any changes so you don't mess anything up. then I rename the original portraits to the following 9000,0 to 9000,9000 and 9000,1 to 9000,9001 and 9000,2 to 9000,9002 etc etc I think you know what I'm getting at.
Then at the very end of the sff I place my new ports for the 9000,0 or whatever you maybe adding then hit save again and your all set. It never fails on my end.

Either just delete the 9000 sprites, and then add them again.

               OR

Start over again, use the character's original .sff file, add the legacy 9000 files don't replace the old ones, delete them first then save over .sff file you currently have.