I know Chef's de France won't let you. I've tried twice. I was on the DxDDP and wanted two appetizers instead of an appetizer and entree. They said with the way Disney reimburses them, that subistutions could not be made and I had to order exactly as the plan states (appetizer, entree, dessert, drink) in order for them to get paid. I told them I didn't care if they entered the most expensive item on the entree list for their records, but I wanted the flat bread. Of course they said they couldn't do that.
OT: I have been able to switch the cheese plate from the appetizer menu for my dessert at several places though (Flying Fish, California Grill, Jiko, and Yacthsman).
Some restaurants might allow it, some might not. Some of the restaurants are more strict than others. Ask when you are there, but it might be best to anticipate that you'll need to order an entree.
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