System Protection jobs utilise the Microsoft Windows Backup Engine and a Shadow Protection warning reported within a job report is a feature in BackupAssist to help protect the historical backups on the destination when the Windows Backup Engine has had some issue reading or writing to it. Typically this will be due to underlying issues like disk hardware problems, high disk I/O, etc. The reason BackupAssist has a “Shadow Protection” option is by default Windows Backup will often delete all historical backups and start again when it encounters this particular problem.
This is described in more detail here – https://www.backupassist.com/support/en/knowledgebase/BA2954-Shadow-Copy-Protection-Mode-protected-the-backup-history-after-a-fault-and-restarted-the-backup.html?cshid=BA2954
This option is not enabled by default as it’s designed as a short-term fix whilst the underlying issue is discovered and as described in the linked article above, the recommendation is to disable Shadow Protection to fully investigate the problem. Also, Shadow Protection will only work around the problem until the Shadow Protection area you’ve defined is full. Once full the issue will start occurring again.
Shadow Protection should not, therefore, be seen as a permanent fix to the problem. It is to be used as a mechanism to protect your current backup versions whilst you identify and rectify the underlying problem that’s causing the Windows Backup Engine to act in the way it is.