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On Plesk for Linux mod_status is disabled on upgrades to improve Apache security. This is a one-time operation that occurs during an upgrade. You can manually enable mod_status later if needed.
There are a number of conditions under which a backup may not complete or may cause minor backup issues:
If disk space at the time of the backup is run is insufficient
A non-storage resource issue at the time of backup
File thrashing (i.e. files that change in the instant that the backup job and the actual zip process takes place)
If you have custom or unique permissions on files or directories that don't enable access to the backup job
If the files or directories are symbolic links
When you say "they are gone" do you mean that you removed the directories and your backups don't show them? It looks like you have a five day retention policy so if the directory in question was removed six days ago, it would not be expected behavior to see the removed directory in the backups for the last five days.