Make apt-get (or aptitude) run with -y but not prompt for replacement of configuration files?

You may use:

sudo apt-get update
sudo apt-get -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confold" dist-upgrade

For only specific packages, e.g. mypackage1 mypackage2:

sudo apt-get update
sudo apt-get -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confold" install mypackage1 mypackage2

Source: http://raphaelhertzog.com/2010/09/21/debian-conffile-configuration-file-managed-by-dpkg/

Avoiding the conffile prompt

Every time that dpkg must install a new conffile that you have modified
(and a removed file is only a particular case of a modified file in dpkg’s eyes),
it will stop the upgrade and wait your answer. This can be particularly annoying for
major upgrades. That’s why you can give predefined answers to dpkg with the help
of multiple --force-conf* options:

    --force-confold: do not modify the current configuration file, the new version
is installed with a .dpkg-dist suffix. With this option alone, even configuration
files that you have not modified are left untouched. You need to combine it with
--force-confdef to let dpkg overwrite configuration files that you have not modified.
    --force-confnew: always install the new version of the configuration file, the
current version is kept in a file with the .dpkg-old suffix.
    --force-confdef: ask dpkg to decide alone when it can and prompt otherwise. This
is the default behavior of dpkg and this option is mainly useful in combination with
--force-confold.
    --force-confmiss: ask dpkg to install the configuration file if it’s currently
missing (for example because you have removed the file by mistake).

If you use Apt, you can pass options to dpkg with a command-line like this:

$ apt-get -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confold" dist-upgrade

You can also make those options permanent by creating /etc/apt/apt.conf.d/local:

Dpkg::Options {
   "--force-confdef";
   "--force-confold";
}

You can find more information and more options in the dpkg manual at http://manpages.ubuntu.com/manpages/xenial/en/man1/dpkg.1.html or man dpkg and i.e. look for "confdef".