Microsoft has confirmed a significant issue affecting its Intune security baseline update process, causing concern among IT administrators worldwide.
The problem, acknowledged by Microsoft in late June, results in custom security baseline configurations being lost when updating to a newer baseline version, such as moving from one annual update to another.
This flaw has left organizations scrambling to preserve their carefully crafted security settings.
Security baselines in Intune serve as templates of recommended configuration settings, designed to help organizations enforce consistent and robust security policies across their managed devices.
While Microsoft provides default values, administrators often tailor these baselines to align with specific organizational needs or compliance requirements.
However, the recent update process has been discarding these customizations, reverting settings to Microsoft’s defaults and potentially weakening an organization’s security posture.
The issue is particularly disruptive for organizations with complex or highly regulated environments, where baseline customizations are critical.
The loss of these tweaks means that, after an update, devices may no longer comply with internal security standards or regulatory mandates, exposing organizations to unnecessary risk.
Microsoft’s current advice offers little comfort: administrators are urged to manually reapply their customizations after updating their baseline policies.
This manual process can be time-consuming and error-prone, especially for environments with extensive or nuanced configurations.
Microsoft has stated that while they work on the fix, they recommend that admins manually reapply their customizations after updating their baseline policies.
The company has promised a permanent solution and will update its official blog with further information as it becomes available.
The Intune team also directs administrators to review the official documentation on updating profiles to the latest version, which outlines the steps for exporting current settings and reconfiguring new baseline profiles.
However, this workaround is far from ideal for organizations seeking automation and reliability in their endpoint management workflows.
This incident underscores the challenges of cloud-based management platforms, where changes and updates can have widespread, sometimes unintended, consequences.
For now, IT teams must remain vigilant, double-checking their security configurations after every Intune baseline update.
Administrators with questions or concerns are encouraged to engage with Microsoft’s support channels, including the Intune support team on X, or to leave comments on the company’s official blog post addressing the issue.
As Microsoft works on a fix, organizations are advised to plan for additional administrative overhead during baseline updates and to monitor communications from Microsoft for the latest guidance.
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