Unattended-Upgrades and autoremove dangerous?

Solution 1:

From the apt-mark manpage:

auto
    auto is used to mark a package as being automatically installed, which will cause the
    package to be removed when no more manually installed packages depend on this package.

manual
    manual is used to mark a package as being manually installed, which will prevent the
    package from being automatically removed if no other packages depend on it.

So yeah, marking the packages as auto-installed can indeed be dangerous.

Under normal circumstances, Remove-Unused-Dependencies in unattended-upgrades or running apt autoremove should not be dangerous. But this of course depends on the following:

• There were no dependency errors introduced in any packages (which may cause undesired removals)
• There are no errors in the manual or auto flags of packages (as you experienced)