@scooby, Thanks for posting in Q&A.
For your issue, here are some information you can check.
1.Please check the device status in Microsoft Entra ID, if it's missing from Intune, but still in Entra ID, it may have lost its management connection. If it's also missing from Entra ID, it could be a case of automatic device cleanup due to non-compliance.
2.Please check the device compliance policy and if there exist some conditional access policy, if possible, could you share the settings of compliance and conditional access policies with us?
3.Try to clean Microsoft Intune app cache totally in target device and unenroll from Intune, after that restart the device follow the link below to re-enroll Intune.
https://learn.microsoft.com/en-us/mem/intune/fundamentals/deployment-guide-platform-linux
Please check above information, if there is any update, feel free to let me know.
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