I had the same thing happen with a PE to J upgrade request next week. Called up and requested no problem. Although my booking is for two people and there is a note on the upgrade page that I have opted for a gate upgrade if original upgrade not requested. I thought gate upgrades were only for solo travellers.
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Had problems for a month or two
send them a feedback thing online saying had issues requesting /changing upgrade request on my June Y+ booking. Got a response saying they are aware of issues affecting Y+ bookings with upgrades but hope to fix it by the end of the week. That was some weeks ago...
not too fussed as there is still time but just annoyed it doesn't work
Had same issues weeks ago, and just tried it seems to be working now.
Requested 2 Y+ -> J for my Aug trip to HKG.
Mine still isn't working for a multi-city Intl booking in April.