From June 1st EK316/EK317 (DXB-KIX) will change to A388.
I have a flight with EK317 on June 2nd in Economy, and it doesn't show me any upgrades to PE, only Business, so I guess it's not a retrofitted A388.
On my return with EK316 on June 10th it shows a possible upgrade to PE.

Checking in expertflyer (free account) it gives me an error messages when selecting PE for both flights.
EDIT: I made a mistake, the flight EK316 will leave on June 11th, not 10th, and shows PE no in expertflyer.

The following picture is shown to me when I visit Emirates. I hope this means a retrofitted A388 will regularly fly this route.