There are a few different possibilities to upgrade at a late stage: You can ask at check in, you can ask in the lounge and (if you are Skywards silver or above), you can even get a 'space available upgrade' on board by asking the cabin crew.
This is all down to revenue management: as long as EK think they can sell an F seat at a Flex+ fare to a late 'walkup' passenger, they would much prefer this to an award upgrade. But obviously an empty seat is bad news for revenue and they would rather take your miles and put you in the seat than let it go empty.
If you tell me what route you are thinking of, I can look up what the loads in F are currently. That of course is no guarantee but we know that some routes are incredibly 'premium heavy' and are very difficult to get upgrades on and others are not that bad.