After a few weeks of use, I have to say the fix -

    [ "/var/lib/apt" -nt "$mycache" ] || [ "/var/lib/apt/lists" -nt
"$mycache" ] || [ "/var/log/dpkg.log" -nt "$mycache" ]

to the /usr/lib/byobu/updates_available script has worked well for me on two 
different systems (both Ubuntu 16.04 with HWE).
After an apt-get upgrade the notification is sometimes still there - but 
hitting a few F5's (boybu status updates) or waiting until the status update 
runs again always clears the notification.

Until you solve it you don't need to reboot, you can simply remove the
cache file to clear the notification with -

rm $BYOBU_RUN_DIR/cache.tmux/updates-available

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  Byobu not clearing update numbers after updates

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