GPO settings are missing after deployment (4324488)

When deploying GPO changes you may encounter that sometimes these changes are not deployed and the GPO ends up with the current settings simply missing the changes that were done to it.

Consider the following scenario:

1. You have a GPO version 1.0 which is blank or it contains settings X and Y.

NOTE: GPOADmin considers the GPO's "last known good/deployed backup" being the deployed 1.0 version.

2. You have an OU where this GPO with version 1.0 is linked to.
3. The GPO goes through a checkout, edit, check-in, request approval step and setting Z has been added during the edit.

NOTE: The GPO has not been deployed yet but a backup has been created during the check-in which is used during deployment.

4. You edit the OU and make any change plus deploy the OU.

NOTE: OU deployments trigger updates of backups of linked GPOs in order to insert link metadata into the backup.

5. You deploy the GPO at this stage and notice that the GPO is blank or the setting Z is missing depending on the initial state of the GPO.

The behavior is by design and occurs in releases prior to 5.14.1. It is caused by the deployment of registered organizational units with linked GPOs which are not yet deployed.