Since the whole refund thing is getting pretty jumbled: Yes, you should have received a refund. My Extra Points Upgrade was at 100%, which cost a total of around 500k coins. I was fully refunded, and I'm sure all of you were too, however if you had a low level of Extra Points, you may not have noticed your refund, or maybe you just blew it all on items and upgrades before you knew why you had the refund.
As for the original question: No official answer has been released as to why the upgrade was removed. I know that some believe it balances the game more, and while that may be true, I think the upgrade was a great way to reward players for the amount of time and effort that they put into Murder. I believe this upgrade should be returned.