If you're sending the grid by post, I'd suggest leaving the unchecked letters blank. I suspect (but don't *know*) the clue's absence will be ignored as the number of I's isn't affected.
Thank you for your phone call and apologies that there was a missing clue in this week’s prize crossword. The clue should have read: 4 A thick, rich soup made from shellfish (6)
I have been told that his should not affect the competition as the iSpy total is unaffected if all the other clues have been inputted correctly.