We've been having problems with the Refund system lately, and are working to correct the issues. You'll notice we currently have Refunds disabled right now. Between the refund wackiness and the Season 2 rewards, we've encountered quite a few problems with our inventory databases.
For now, feel free to re-spend your IP on new exciting things, but don't grow attached to your returning champs. They will de-materialize once again when we fix this issue. So, don't buy skins for them.
Let me repeat that, in a mighty, loud, All-Caps voice: DO NOT PURCHASE SKINS FOR YOUR MYSTERIOUSLY RETURNED CHAMPIONS.
But otherwise, proceed as normal, and feel free to use the Champ and spend the IP.