Removing all Missing Backup Files from Backup
This shows how to remove all backup files that are missing from a backup. The cmdlet will remove the missing backup files and all files linked to it from the configuration database and from disk.

#Run the Get-VBRBackup cmdlet. Specify the Name parameter value. Save the result to the $backup variable
$backup = Get-VBRBackup -Name "Daily backups"
#Run the Remove-VBRBackupFile cmdlet. Set the $missingfile variable as the BackupFile parameter value. Provide the FromDisk parameter.
Remove-VBRBackupFile -Backup $backup -FromDisk

Add the -WhatIf parameter to check what will be done without applying anything

$backup = Get-VBRBackup -Name "Daily backups"
Remove-VBRBackupFile -Backup $backup -WhatIf -FromDisk