What you have found is true of most (all?) EK routes via DXB. Mileage required is based on geographic sectors of the origin and destination.

When the second sector became available, what you could have done was cancelled the first sector upgrade and the miles would have been returned to you. If availability then showed on both sectors at that point, you could have upgraded for the lower amount.

Where this can fall down is the cancelled sector might not automatically go back in to the upgrade bucket, so you're back to square one. However if you do it over the phone, they may be able to hold it for you.

If you call them now and explain you want to cancel and rebook as one upgrade, they may be able to do that.