As far as I can tell, this can be closed.

Please make a note in man file or project docs under "troubleshooting" that -- 
if ~/.pypar2/prefs.xml is 0 bytes, make some room on your drives, delete 
~/.pypar2 directory with command 
[ sudo rm -rf ~/.pypar2 ] 
then do a reinstall 
[ sudo apt-get --reinstall install pypar2 ]
After executing Pypar2, the prefs.xml file will be re-created, and you are good 
to go.

Thank you, thank you, thank you!

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https://bugs.launchpad.net/bugs/1031567

Title:
  pypar2 will not load, errors from commandline...

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