Assuming that the article is accurate, and as you stated, that is a big "if", I think this patrol was intended to be the re-innauguration of the Argentinian submarine service as a capable force.
To make this possible, the submarine had just been given a 12 million dollar re-fit. This figure seems too low for a full re-fit as I have read of other nations spending tens of millions on sub re-fits due to the complexity of the work and the need for precision.
In either case, the submarine puts to sea after a some what fitting re-fit. There is a lot of pressure to complete this patrol and a completed submarine must be done submerged. So, even after an initial round of problems, the crew is ordered to complete the patrol submerged if at all possible?
As a side note, Chile has brand new submarines and Brazil either has new ones, or has them on order. There is a historical rivalry between Argentina and both these nations. This may have increased pressure to demonstrate that: "Hey, our submarines are old, but still lethal"
Crush depths are secret. Rather, the only published depth is a maximum diving depth for normal operations- usually about 1,500 feet type figure. The published figure, however, is not the true diving depth.
Good point about water on the batteries releasing a poisonous gas (Chlorine?). Perhaps there were two series of malfunctions:
A. The initial battery short. The crew solves the problem. Radios the problem in: Shore- "Ok, but we really need for this patrol to be successful, stay submerged... ."
B. The crew then uses the diesel via the snorkel to recharge the other battery when it runs low. Another malfunction occurs with the snorkel. This may have resulted in poisonous gas, fire, diesel fumes, air pressure imbalances, water taken on etc., or a combination of several of the above. A well trained crew with good safety equipment could save the submarine. The crew, however, is not well trained and many things are not fully working. They get overwhelmed.
