I need to book a round trip for 2 passengers on an EK flight from the US to Male with a stopover in DXB.
I don't have enough points to book in J and the J ticket prices are too high. Instead, I decided to book the flights in PE and then upgrade to J with points.

Each of the flights had J Saver class seats available, so I should be able to upgrade. I went through the booking process and booked the PE tickets. I then immediately went to the "Upgrade with Points" tab. It showed upgrades available on each flight and the points required. Next I went to my Chase and Capital One accounts and transferred the necessary points to my Skymiles account. The points did transfer right away, but were not showing up to pay for the upgrade. I had to sign out of my Skymiles account and then sign back in and now it did show my transferred points. When I went back to "manage my flight" and went to the "Upgrade with Points" tab again, it was showing "no upgrade available" on one of the flights.

I had heard that you really need to execute the upgrade process immediately after booking and in the same session and apparently that is true.
Maybe there was another way to refresh my points total without signing out?

Anyway, I decided to just take advantage of the free cancellation option and cancelled the entire booking. Once my refund is processed I'll go back and book it again. The points are already sitting in my Skymiles account now, so I can go straight to the upgrade page after rebooking the flights.

Did you call them?

Sometimes online has problems.

It needs to be J Saver Reward seats available, not regular J Saver seats.

there isn�t premium economy to male so you�ll need to call them

Ahh! Thanks 101 for that clarification!
I know there's no PE on the DXB-MLE leg, that's fine. I'll try booking again after my refund clears and if I hit another snag I'll try calling them.