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Equipping items should remove the item position from the item.
If two items have the same inventory space place "saved", and there is no free space to the right, unequipping makes the two inhabit the same space, so one seemingly disappears. I would expect it to be moved to the left instead.
To recreate: put x slot item in last free inventory space, equip it, put another x slot item in the same space, unequip the first one. Now the first two overlap.