When a site has "Zero Downtime Deployment" enabled, any File Backups only back up the symlink, and not any actual site files. This can easily go unnoticed as no alert is issued, because the backup task thinks it has completed successfully.
From support ticket #6303
File backups always silently fail when using Zero Downtime Deployment
Dennis moved item to board Planned3 months ago
James Cocker moved item to project Site Level Requests3 months ago
James Cocker created the item3 months ago