Just hopped into an ARAM and got Nunu, so I used one of my 2 rerolls to get Oriana. Then someone left the game and I was placed in the queue again. I get into a new match and when I looks that the number of rerolls I have it is down to 1 instead of 2.
It's not supposed to do that. Normally it works just like Skin-Boosts when someone dodges or you even you should get refunded.
I'm having this exact problem as well.
It's not missing permanently. Finish an ARAM game or close/reopen the client to get them back. If you search this very board, you will find tens if not hundreds of the same post, most of them with a reply from me saying this exact same thing.
