1) You need to be a local admin while performing the backup, and the restore, in order to back up the data stream even though you don’t have access to the encrypted files.

2) If a policy is disabling EFS on the recovery workstation, ntbackup won’t tell you that it can’t create the encrypted files because EFS is disabled. No. It will simply SKIP the files. So if you have files that get skipped, try to manually create a folder and encrypt it. It has to work else you will not be able to restore the backup properly..

Trying to enable EFS on a specific OU, while it’s disable at the top of the structure or domain?
Recovery certificates from two different GPOs mixing up instead of being replaced?

Overall EFS GPOs looking like they aren’t merging properly?

Well, it’s not because EFS GPOs are supposed to behave like black magic. Turns out there’s a bug, Microsoft’s aware of it, but doesn’t think it would be a good idea to FIX IT on Windows XP and 2003.

Thankfully, all it means is you need to edit your GPOs from a Vista, 2008 or Windows 7 machine.

KB : EFS may not be enabled expectedly after you disable a policy and this policy turn off the EFS feature

Opening my EFS GPOs in Windows 7, switching the Allow/Don’t allow and applying the ‘change’ fixed my GPOs. A few minutes later, and stuff was behaving like it should’ve been… Can I have those wasted hours of my life back, Mr. Ballmer?