Running version 3.3.x, F5 load balanced 3 front ends, glusterfs, memcached for application cache.
We keep 4 semester's worth of courses on our production server with approximately 800 in each. They are all organized by Semester and then Subject. We only use the course-level backups 3x per year to 'archive' the oldest semester.
I use a minor code hack to direct the automated backup to backup just one category each semester and we mount a windows' share with a lot of storage to our linux box so the backup files get written directly to the share, not the Moodle instance so there are no storage issues.
Once the backups are done we delete that semester's worth of courses from the production server.
This process works very well for us to keep the courses current on our production server while maintaining backups for those instructors that need copies of older courses that they may be re-teaching. Super easy to browse to the windows share to restore backups on request.
If anything you can use the hack to target categories to prevent an entire system backup:
1. moodle/config.php
ADD
// List category id values to be included when backup runs
$CFG->backup_category = array(65);
2. moodle/backup/util/helper/backup_cron_helper.class.php
ADD
// Check for categories to backup
if (!empty($CFG->backup_category) && is_array($CFG->backup_category))
{ $rs = $DB->get_recordset_list('course', 'category', $CFG->backup_category); }
else
{ $rs = $DB->get_recordset('course'); }