Package: apt Version: 1.0.9.8.3 when there are invalid or expired apt repositories configured, ALL other apt repos will not be updated.
In my case: CRON-APT LINE: /usr/bin/apt-get -o quiet=1 update -o quiet=2 E: Release file for http://ftp.uni-koeln.de/debian/dists/jessie-backports/InRelease is expired (invalid since 8d 18h 50min 50s). Updates for this repository will not be applied That message implies, that updates for this repository will not be applied (but others will!) But no packages are installed. Disabling the expired repository makes "apt-get dist-upgrade" install all the outstanding packages that have been release in the last 8 days (since the mentioned repo expired). Enabling the repo again hides all the outstanding updates right away.