Your Gardevoirite has to be somewhere, items can't just disappear like that. Which means that there are a few possibilities of where your Gardevoirite could be.
- Try checking your Gardevoir again, your Gardevoirite might be on your Gardevoir and you just didn't realize that it was there.
- If your Gardevoirite isn't on your Gardevoir, check the other Pokemon in your party, you might have accidentally given it to one of them.
- Try the PC, you might have accidentally given your Gardevoirite to one of the Pokemon the the PC.
- Check your bag, your Gardevoirite might be in there.
- Your Gardevoirite could have been traded away, this could be done by a sibling being mean to you, or by accidentally putting a Pokemon holding your Gardevoirite up onto the GTS, either way, it could be extremely hard, if not, impossible to get it back.
Those are the only things that I can think of, if it isn't one of those, it's probably a glitch.
Hope this helps, and good luck finding your Gardevoirite!