Were the sub's Diesel engines actually connected to her screws, or did they run generators which fed electric motors, through the batteries? With batteries shorted out, there would be no way to transfer the diesel engines' power to the propellers.
On the surface, dead in the water, in 20 foot seas - not a good scenario.
Diesel boats switch between battery and diesel power. They have to run a minimum of snorkel depth in order to charge the batteries with the diesels as they have to need air to cycle to prevent CO buildup.
If the seas were 20ft they would have been tossed around like a bingo ball if they completely surfaced, and the snorkel may have been taking on water. Either scenario could very well have ended up with her unable to power forward in rough seas and foundering. I think this is the most likely scenario - the loss of communications ties with that weather scenario as well.