I actually did it the other way, but it was early on so I don't remember if it cost me anything in game. You can get a key for both platforms from Frontier. Ironically, I just bought an Index and want to go back now.
Would it be possible for you to launch Steam, not Steam VR, but Steam, press the '+ Add a Game' button on the lower left corner of the Steam screen, locate ED from the list that comes up, select ED, and add it to Steam? After that, I imagine that ED will be listed as one of your games when you then launch Steam VR. I am not positive about this. I hope it helps.
In case this is helpful to someone else in the future, this was easy. Through frontierstore.net, I was able to claim Steam activation codes. Then I just installed the Steam version and launch it from there.
I do still have an issue where the Oculus app launches whenever Elite starts, but after I close it once it stays closed.