Oops! Sorry ... wrong URL:
/admin/settings.php?section=backupgeneralsettings
Site Admin Menu -> Courses -> Backups -> General Backup Defaults
version 2.6.x of Moodle.
Files just don't 'disappear' for no reason ... not that you did anything wrong, but from what you've described don't think there is or has been any similar posting about such an issue that didn't involve some change that had un-intended consequences.
You might have to resort to mysql queries of the DB to see if there are references in DB:
select contenthash,component,filearea,filename,filesize from `mdl_files` where `filename` like "%.mbz%"
The contenthash output from above will show something like:
0e6a1fab7eecb82c5bc8fbd968ec769687618f8c
and one can then find the file using a filebrowser in moodledata/filedir/0e/6a/ to see if there is a file by the contenthash name 0e6a1fab7eecb82c5bc8fbd968ec769687618f8c and if it is a zip
Like so:
file -b /var/www/moodledata/filedir/0e/6a/0e6a1fab7eecb82c5bc8fbd968ec769687618f8c
Zip archive data, at least v2.0 to extract
Indicates the file is a zip.
Running autobackups? Is the directory for that outside of moodledata? Those won't be seen in restore screens.
'spirit of sharing', Ken