I've changed mine countless times and it always applies it to the changed reservation. Last night I changed it again (last time, I swear!) and had to pay $53 because the room was slightly more expensive.
The only time it's been a cancel/refund situation was if I changed from room only to package (or the other way around). Just changing resort or category the deposit transferred over - I just had to pay the difference if the new room was higher.
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