Is your battery pack protected by some sort of battery management system or PCB? If so, it may have kicked in and "protected" your cells to some extent. I have taken apart Li-ion battery packs that read very low voltages or even zero voltage, but after removing the PCB, and VERY CAREFULLY disassembling the pack into its individual cells, the individual cells had a normal voltage and charged and worked just fine.
Can you measure the individual cells directly and not via the balancing wires? Although now that I think about it, the balancing wire measurements that you took should bypass the PCB so it is not a good sign that you got a reading of 0.
Edit: Upon further thinking I realize that the balancing wire could have one of its leads attached to the PCB (either the positive or the negative balancing wire) and if the PCB has kicked in and blocking access to the cell, it will read 0
How long was the pack short circuited? If it was only a brief period (a couple of seconds or less), then I would be suspicious of your reading of 0 volts, especially given that the other cell has a normal voltage reading. Was the pack old and near the end of its life anyways?
The safe thing to do is to recycle the battery and get a new one as li-ion are dangerous to play with!
BUT.... if the protection circuit has just kicked in then putting it in the charger for a few seconds might "wake it up". My understanding however, is that most protection circuits that kick in for short circuits, usually "wake up, or unlock" shortly after the circuit is no longer shorted. BE SAFE. Good Luck.