We all feel your pain with this as backups are critical as are the inevitable restore of them. I can only speak for myself as I mentioned here in a previous post the backup/restore procedure has been flawless in my environment. https://forum.virtualmin.com/t/outstanding-backup-restore-virtualmin-functionality-feedback/121268.
For the benefit of others and my future self and hopefully you, I will document below my complete settings I have used for years using “Backup and Restore > Scheduled Backups”.
- Virtual Servers - Select “All virtual servers”
- Features and settings - default “Backup all features”
- Destination and format - I use a local directory for quick individual virtual server restores and copy to the cloud for disaster recovery (See 4 below on that part).
- Schedule and reporting
- Add your email for reports
- I use simple daily/midnight schedule
- I use rclone “Command to run after backup” to send all backup files to a cloud account
Finally this includes mysql dbs as well as respective users and I confirm regularly that all restores as expected. If you have a similar setup (I use Almalinux 8.5) and experienced the issues you note then that would indicate an issue specific to your installation unfortunately.