the second effect (when you short the input terminals together, it's not the battery terminals shorting together, it's the transformer winding shorting that's causing it) is because you are collapsing the magnetic field, and in the process dumping a huge amount of current through the primary (the primary leads being shorted together) this induces a large current in the secondary, and a very large voltage across it as a result, however, this can't be good for the battery, since it's driving a short circuit for a moment. it also may not be very good for the secondary winding, since the voltage you're producing may be enough to break down the enamel insulation on the wire and cause a shorted turn.
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