In case you need to override manually

$ sudo rm /usr/share/indicators/messages/applications/evolution
$ sudo bash -c "echo /usr/share/applications/thunderbird.desktop > 
/usr/share/indicators/messages/applications/thunderbird"

-- 
"Evolution Mail" shouldn't appear in indicator-applet when the user has 
selected a different email application in System>Preferences>Preferred 
Applications
https://bugs.launchpad.net/bugs/429569
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