Upgrade first or change first?
 

A not so hypothetical situation:

A ticket needs to be changed to a different flight, as well as upgraded. Both flights have I inventory, but the original class of booking is not available on the flight to be changed to.

In this scenario, I'd imagine it makes sense to first upgrade the ticket, and then change flights. Would this work however? Or would they still charge the fare difference as upgrade by miles still limits you to fare rules of your original ticket? Anyone who has experience doing this?

Upgrade first, then change.
I have done it before.

Assuming this is the first sector, I 'think' you have to rebook into the original booking class on the new flight (and pay any fare difference) and then u/g into the fare bucket you want - I for u/g to Biz. I had to do it this week and, even though I had already upgraded to Biz on my original flight, I had to re-book into Y on the new flight and then re-upgrade.
It seems a lot easier to do it at an Emirates booking counter than over the phone.

So no way to avoid the fare difference then I guess.

Well, the person who needed to do this had already paid the difference and upgraded, but it ended up being a 3 class operated as a 2 class. First flight on Emirates, and in a first class seat. Now why couldn't my life be like that? :P