OK, so maybe it was more than just once
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Luckily, by “there were no LMDs left,” we of course mean that there were LMDs left, so the Fury who was killed was an LMD.
Finally, Fury’s shortest “death” would have to be Secret War #5, where it is revealed that Fury wiped the memories of a bunch of superheroes after they did a mission for him. Now, a year later, the heroes are being targeted for revenge (and they have no idea why). Wolverine, as you might expect, is not a fan of his mind being messed with…