No idea, but short circuiting something for a very short time of 1 sec is an eternity for electronics 
You did not give details (e.g. a complete hand-drawn schematic) that shows where the battery fits in and what else is connected. If that battery powered your board and you short circuited the battery and nothing else was connected, there should not be a reason why it would not keep on working.
So please provide the details.
If burning the bootloader works but uploading fails, I suspect that you permanently damaged the 328P microcontroller and personally I would take the loss and buy a new one 328P.