Skin Loot Question

I opened a chest and got an Annie skin and upgraded to permanent. This was my first time upgrading to a permanent skin so I'm not familiar with the process, but the skin shard is still in my loot. It's permanent, and I believe I can use it (as it says "owned" although I haven't yet tried it because I don't have the time today), but the shard hasn't disappeared. Is this normal? I'd rather not have it there because there's still the option to reroll into another permanent skin or disenchant and I don't like that there's a chance the skin could be lost either of those ways.

Do upgraded skins just stay in your loot forever? I'd appreciate if anyone can tell me.