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How are you going to update your Ubuntu version to 16.04? Are you going to use the packet manager to upgrade your OS or would you rather do a clean install from installation media?
Whenever you start from a fresh new Ubuntu 16.04 installation, you will only get the option to install ROS Kinetic (or higher), because ROS Indigo does not support Ubuntu 16.04. (Please see #q245288, if you really want to install Kinetic and Indigo in parallel.) If you perform an OS upgrade through the Ubuntu packet manager, then your packet manager will supposedly remove ROS Indigo automatically unless you installed ROS from source. The packet manager should know, that the ROS Indigo packages will no longer be compatible with the new OS version.
For me, a fresh new Ubuntu installation always appeared to be the safest way to upgrade from ROS Indigo to ROS Kinetic, so I have never tried to use the automatic OS upgrade.
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