Running with `auto-package-update-delete-old-versions t` leaves some packages uninstalled

[TLATER]

When updating with auto-package-update-delete-old-versions t quite often a number of packages will not be updated, but still removed from the package directory, resulting in complete removal of the packages.

This tends to leave me in a state in which I can't use my editor, since it's pretty prone to removing helm and that in turn leaves me unable to execute any commands that aren't bound to keys.