I'm having a similar problem - I purchased an 800L skin, now the item is not only missing from my inventory, the record of purchase is gone from my inventory, the merchant's inventory, and her redelivery terminal's records. All of my other purchases from her store (that I made at the exact same time) are still there ($1050L worth, to be exact) - but because that particular purchase is missing, I no longer have the skin that goes with the shape, hands, feet, and appliers I bought.
Does anyone have a way to fix this? Because until I know why this happened, I'm not really comfortable dropping another $800 for the skin if I might not get to keep it.