Had the same thing happen to me - upgrading friends with 2012 expiring GPUs, when the Premier Desk/1K Desk agent had trouble applying them. She saw the inventory, but needed the "help desk" to assist with pulling the GPUs and applying them. It took 45 minutes. By then, 1 of the two segments on the itinerary had dropped from R2 to R1 and they could only upgrade the shorter segment for both travelers. You'd think a Service Director could have maybe gotten another R seat opened up for me, but no - it was too bad for my friends and I because their systems couldn't process the request fast enough.
So all you people cheering for the fact a CPU might have gone through - this same thing can happen to you, too, when you want to use instruments, and won't you be loud in the forum with your gripes then!