I did that last year with Aloha. Pre-paid, then add DDP. It was a nightmare (for me) to get refunds. I asked the concierge and at check in, they both told me it's OK, just talked to the hosts at venue. What should happened is that at the restaurant, the hosts are supposed to switch out the pre-payment with your DDP in their system (aka you get a refund on your CC). That didn't happen. The host just confirmed that we're on meal plan. On our last day I noticed the refund still didn't happen and we had leftover TS. Took me literally 2 hours at check out, dealing with the Manager. He had to make multiple calls too. The system won't let him override the payment section, so it's really the system that couldn't handle this switch *after* the meal was done.
1 more thing. I tried changing this over the phone pre-trip (they couldn't), talked to hotel front desk beforehand (no access to DDP system), Guest service (they could only tell you # of TS left..etc, but couldn't change plan) and referred us back to concierge who told us to talk to restaurant. It's a rare Disney failure.
Moral of the story, don't wait till check out to sort this out. Make sure the host change the payment to DDP before you sit down. Check cc the day after the dinner. Shouldn't take longer than 24 hours. And watch your TS / snack counts.