You can still change dining plans (or have a dining plan for only part of your stay) if you have multiple reservation numbers for your stay.
As I understand, that would require a split stay or, at the very least, changing rooms within the resort.
For future reference, if you have this in mind make sure that MS books your rooms under different reservation numbers. We have a split stay in May/June and are considering alternating dining plans but are not sure yet. We have two reservation numbers. However, I have read that it is possible for MS to book a split stay on one reservation number. Not sure if this is the case. It could be that MS has the option to book one stay within the same resort (but in two different room types) as one or two reservations.
Can anyone clarify this? Can MS put a split stay between two resorts on one reservation number? Also can MS put a split stay within one resort (different room class) on one reservation number (not sure if this would be referred to as a split stay)?