You simply edit your table so that you have the new prompts in it. How you want to show they're substitutions is up to you. You can just replace them on the table and not mention it or you can cross out the originals and add the new ones or you can label them as Prompt #X [whatever] replacing Prompt #Y [whatever].
When you post the fic, in the header where it says the prompt say that you're substituting whatever your new prompt is for the old one. I'm not bothered about how exactly you phrase it I just need it to be clear so that if I need to I can check through and see how many you've changed.