I can attest that this is the way it worked this year. I had clients booked on the July 6th Baltic. Military rates came out on May 15th. Because they were well within the 90 days out and already paid in full, I called Disney before I let them know about the discount, just in case.
There were no penalties, they just switched them to the discount and they ended up with a refund on their credit card of more than $13,000 for their two cabins.
