How do you use a promotion code after the sales order is invoiced, I.e. customer forgot to provide the promo code to the call center and now they called back to get the discount.

you should be able to apply the promo code to the existing SO (not invoiced yet). Refer to suiteanswer 96552

How about cash sale? Some customer requires prepayment

may be issue a credit memo

96552 is while creating a SO not existing one, cash sale doesn't create credit memo it creates Cash refund

isnt that basically the same thing 🙂

yeah i guess 🙂 but the tricky part is you have to create the refund for the whole transaction, I don't want to create for whole transaction, I just want to give them the discount that they forgot to use

Create a separate credit memo for that discounted amount.