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Can you elaborate please?
The Backup scope, your desired result, and the actual result and maybe a ticket number where there are some diagnostic logs would really help here.
I guess you're referring to "GLOBALROOT" paths our software shows when encountering VSS-related errors. The problem here is that in very rare cases VSS can't upload EFS-encrypted files even with the correct service account. The issue will be fixed in version 6.3.1.
For now, as a workaround, I can suggest to create a separate backup plan for those files and disable "always use VSS" option, that'll solve the problem.
You have options to either Keep EFS Encryption or Decrypt EFS files at backup time. The new feature is only available when using the New Backup Format.