I'm still not completely sure what caused the issue, but I selected an item (enchanted diamond sword), hovered over another item (enchanted diamond pickaxe) and left-clicked and dropped on what I think was the same frame. When I closed my inventory, the pickaxe was on the ground but the sword was completely gone. However, when I placed another item (2 sticks I think) in the slot where the sword was and then selected the sticks again, I was now selecting my sword which had reappeared in my inventory. During the time I didn't have the sword, the slot seemed to be completely empty. My inventory and the sword seemed to work completely fine afterwards.