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>>> Not leaving hatches open that could potentially sink a ship, particularly a submarine, is basic common sense.

Hatches are left open all the time. This sub was not at sea but in harbour. A sub is an enclosed/confined space. While in port it would have been undergoing all sorts of maintenance work. Hatches are left open for ventilation, access, even to run power cords for electric tools. It is not unusual for someone welding stuff inside a ship to require the nearest hatch to be left open for a long period of time.

Do submarines have "lockout-tagout" procedures for this kind of thing?

They are supposed to. Whether such safety procedures are actually used is another matter. Submarines, like everything else in the military, are great at looking very professional on the outside while being total chaos on the inside.

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