Well it took a while and a few back and forths but Emirates has agreed to credit me the full tier miles for the flight. I didn't have to pay anything extra for that.

At the end of the day if this is EK's policy thats fine, they just need to communicate it. Nobody is going to check to see if they've been downgrade (fare class wise) unless they know its a possibility. I've made 100's of changes online (I do all my booking/changes online where possible) I'm surprised this is the first time I've had this happen.