We're back, I finally found this thread again, the upgrade worked, and we got full credit for the 10 day NE. That's the short version.
Long version: After checking in and picking up our (10 day NE) tickets, we headed over to Epcot and used those tickets (which were still on our room keys) to enter the park. Dh and the kids went on S:E, and I went to Guest Services. I explained that I wanted to upgrade our MYW tickets to AP's, and was told I should wait until the end of the trip or else risk being locked out of my room and losing all my dining credits. I smiled, and explained that I appreciated his concern, but I really wanted to do the upgrade now so I could take advantage of parkhopping, AP discounts, etc. He called someone else over, who said the same thing, then added I could only get credit for what I'd paid for the tickets, which was $359.97, and not the gate price, which was $465.41. I continued smiling and explained that actually, because I'd already used the tickets, they are supposed to bridge the gap between the discounted price and the gate price, and credit me full gate price.
The second CM disagreed with me, but told the first CM that he could go call guest relations to find out for sure. So he left, made the call, and came back a few minutes later confirming everything I'd just said. When he noticed the difference between what I'd paid and the gate price, he said in shock, "that's over $100!" He began the long process of separating the tickets from the room keys, ringing up my credits, charging me for the AP's, applying my credits and finally printing out my AP's. He was still a little worried about messing up my room keys, but I assured him that we had done this before without incident and, in the unlikely event of a problem, I was sure we'd be able to work everything out back at the hotel.
I am so glad that I found this thread again also. I was reading it back when you guys were discussing it and hoping that I would remember the details. My 2 DDs & I are going in July & have 10 days NE on the 4/3 plan actually bumped up to 10 nights at POFQ. I would so love to be able to do this. I am going to print this out and memorize the reasons you quoted. I may try at guest service in MK as I have found them to be very knowledgeable about such complicated transactions.