I have tested this by creating 2 versions of a package where the first
creates the configuration file /etc/test/test1.conf (test1.deb) and the
second creates the configuration file /etc/test/test2.conf (test2.deb).
On installing test1.deb and then test2.deb only the file
/etc/test/test2.conf exists so dpkg does clean up obsolete configuration
files. But it seems this does not happen if a package gets reinstalled
as sayed in comment #1.

** Changed in: dpkg (Ubuntu)
       Status: Invalid => New

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https://bugs.launchpad.net/bugs/1569926

Title:
  Package seems to got modified without changing its version number

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