I have not seen the same problem again. The is more then 4 years old. I
think it can be closed.

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https://bugs.launchpad.net/bugs/221048

Title:
  Preferred Applications - Web browser/Mail Reader not automaticaly
  updated to new standard

Status in “xdg-utils” package in Ubuntu:
  Incomplete

Bug description:
  Steps:
  -Updated sources.list from gutsy to hardy
  -Reloaded list in Synaptic
  -Marked all upgrades
  (no error messaged during upgrade)
  -Rebooted
  After doing this, mozilla-firefox and mozilla-thunderbird are no longer 
recognised.
  But these where still registered in the "Preferred Applications" dialogue. 
Thus no links where opened.

  I think this problem should be recognised and fixed when the packages which 
contain mozilla-firefox are removed.
  So the preferred applications are automatically updated, not only to "firefox 
%s" but also the correct application is selected in the combobox.

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