Yes, this needs to be sorted out.

I was looking at the source code of the software-properties package and I may 
have found the problem.
In the file softwareproperties/gtk/SoftwarePropertiesGtk.py there is this 
method around line no. 991 (sorry if I'm not supposed to put code here):

    def on_close_button(self, widget):
        """Show a dialog that a reload of the channel information is required
           only if there is no parent defined"""
        if (self.modified_sourceslist == True and
                self.options.no_update == False):
            d = DialogCacheOutdated(self.window_main,
                                    self.datadir)
            d.run()
        self.quit()

This is where the program should ask the user if he wants to update the cache 
(the Kde version should have something similar), but that is not happening.
If I remove the "self.modified_sourceslist == True" part of the condition, it 
works, so I believe that variable is not set correctly (I suppose this variable 
should "tell" if the sources were changed).
I'm not an expert in Python, so it would be better if someone else checked this.

Now, for the Software Center, I haven't tested if it's still necessary
to re-open it.

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https://bugs.launchpad.net/bugs/782953

Title:
  Software Center doesn't detect changes in sources until update-apt-
  xapian-index is ran by cron

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