The Intune support team tried to get the Config Manager team to pick up the ticket, but they refused. I did notice this advisory in the admin console yesterday. Not sure if it's related.
Some admins' co-managed devices are missing endpoint protection policies after applying a Configuration Manager update - IT791333
This issue specifically impacts endpoint protection policies on co-managed devices managed by Microsoft Intune where admins have updated to Microsoft Configuration Manager version 2403 or 2309 HFRU. Other policies and devices managed in Microsoft Intune aren't impacted.
Our fix has completed the initial validation stages and we're deploying it to our internal test environment for further validation. Additionally, we've identified a short-term mitigation which should provide relief until our long-term fix is in place and included the information regarding this short-term mitigation in our "More info" section. We expect that our fix will begin deployment to your environment on Monday, May 13, 2024, and should complete and resolve the issue on Friday, May 17, 2024.