I know update-manager usually doesn't change usersettings, but this case
is special in that the resulting behaviour has been changed already by
the bugfix in gnome-panel and changing the users setting to make the
default nautilus again automatically would result in the old expected
behaviour for most people. I.e. it would lead to less percieved changes
in usersettings than when doing nothing.

Michael: with upgrade note you mean a message displayed during
upgrading? And then a button that when clicked would fix this for the
user? That doesn't sound too bad either, although this will be hard to
communicate understandably without getting too technical.

-- 
opening a directory using an application change associations incorrectly
https://bugs.launchpad.net/bugs/260492
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