Your first question is not making any sense to me.
If you have FTM2012 Open, then go to File > Restore > Browse to the file and click ok, the file should open in the FTM2012 that you have open. I haven't a clue as to why you have another version popping up.
As for your second question, did you not check the dataset in your Extended Chart after you ran it to see if was only the dataset you wanted to export (ie either Mom's Side or Dad's Side)? Did you disconnect your mother from your father and their children before you ran the chart?