Microsoft Intune Glitch Resets Security Baseline Customizations: What You Need to Know

A Crucial Vulnerability Exposed in Endpoint Configuration Management

Microsoft has confirmed a major flaw in Intune, its cloud-based endpoint management service, that could compromise enterprise-level security customizations. The issue affects how administrators update security baselines—those preset policies designed to enforce secure configurations across devices. Specifically, when IT teams upgrade from older baselines like 23H2 to newer ones like 24H2, their customized settings are lost and replaced with Microsoft’s default values. This oversight puts sensitive configurations at risk and forces administrators into repetitive, manual reconfigurations to maintain their security posture.

Customized Settings Wiped During Intune Security Baseline Updates

Security baselines in Microsoft Intune are essential tools used by organizations to enforce recommended security settings across Windows devices. These baselines are built using device configuration profiles and leverage Microsoft’s Configuration Service Provider (CSP) framework to control settings like BitLocker encryption, password complexity, and user authentication rules. Administrators frequently customize these baselines to align with unique compliance requirements or operational preferences. However, an update bug has emerged that resets these custom configurations when transitioning to newer versions, such as from 23H2 to 24H2.

The issue stems from an update mechanism introduced after May 2023, which aligns baselines more directly with CSP configurations. Unfortunately, this new format fails to preserve settings that deviate from Microsoft’s recommended defaults. When updates are applied, those manual changes are wiped out, reverting the entire configuration to its standard state. This disrupts organizations that depend on finely tuned security rules and leaves them scrambling to reapply changes manually.

Microsoft has acknowledged the issue and offered a temporary workaround. Administrators are advised to reapply their custom settings manually after each update. They should also consult the Microsoft Learn documentation to understand how to export current settings and streamline reapplication. Microsoft is currently working on a permanent fix, with updates promised through official support channels and blog posts.

To prevent future disruptions, Microsoft recommends several best practices. IT teams should test updates on duplicate profiles before applying them to live environments, export their settings to CSV files for tracking, and roll out updates in stages. Organizations are also encouraged to monitor Intune baseline version changes and consider using automation tools like PowerShell or Microsoft Graph API for managing configurations at scale.

This incident underscores the complexity of maintaining endpoint security and the critical need for proactive update strategies. While Microsoft refines its baseline architecture, IT administrators must stay alert and methodical to avoid security regressions during updates.

What Undercode Say:

The Risk Behind Configuration Management Blind Spots

This glitch in Microsoft Intune reflects a broader challenge within enterprise IT infrastructure—balancing automation with control. While security baselines offer a scalable method to enforce policy consistency, they also introduce dependency on vendor updates. When those updates fail to respect prior customizations, they don’t just erase settings—they erase institutional knowledge, compliance efforts, and potentially, security defenses.

Security baselines aren’t mere templates; they are strategic tools tailored to organizational risk postures. Losing those custom settings can lead to misalignments with regulatory frameworks like NIST, HIPAA, or ISO/IEC 27001. For sectors like healthcare or finance, where configuration specificity is legally mandated, this glitch isn’t just a nuisance—it could become a compliance violation.

What’s particularly problematic is that the affected update mechanism went unnoticed for months. Organizations upgrading their baselines in good faith were unknowingly rolling back critical defenses. And while Microsoft has issued a workaround, it’s a reactive step requiring manual labor—something most enterprise IT teams strive to minimize in favor of automation.

More troubling is the lack of rollback functionality. If an admin updates a baseline and doesn’t realize the custom settings were lost, those devices could remain non-compliant until a security audit uncovers the gap. In a zero-trust security model, that’s unacceptable.

The workaround itself poses logistical challenges. Exporting CSVs, comparing settings, and reapplying them after updates adds operational drag. Small teams may not have the bandwidth to perform this consistently across fleets of devices. While scripting via PowerShell or Graph API offers some relief, it assumes a high technical skill level and introduces another layer of complexity.

This issue also raises questions about Microsoft’s internal QA processes. Introducing a fundamental change to how baselines store configurations—without preserving legacy customizations—should have triggered more robust migration safeguards. At minimum, admins should have received warnings before settings were overwritten.

The bigger takeaway? Organizations need to treat baseline management as part of their broader configuration lifecycle strategy. That means version tracking, backup procedures, and automated diff checks should become standard. Ideally, Microsoft should integrate these capabilities natively into Intune, offering a “custom settings retention” toggle or a “what changed” preview before finalizing an update.

This vulnerability, though currently addressed with a temporary fix, reinforces why endpoint security can never be a set-it-and-forget-it process. It’s a continuous cycle of validation, verification, and vigilant change control. Until Microsoft provides a permanent solution, the burden is on administrators to remain skeptical of updates and treat every configuration change as a potential risk event.

🔍 Fact Checker Results:

✅ Microsoft confirmed the issue on their official support and documentation platforms.
✅ The bug affects all baseline versions released after May 2023.
❌ There is currently no automatic fix; manual reapplication of settings is required.

📊 Prediction:

If Microsoft fails to roll out a permanent solution before the next major Intune baseline release, large enterprises may develop third-party automation tools or revert to manual scripting to handle configuration persistence. Expect rising community interest in open-source tools that can export, compare, and reapply Intune settings with minimal user input. This incident may also push Microsoft to integrate version comparison and setting diff tools directly into Intune’s native dashboard.