@jm, Thanks for posting in Q&A.
From your description, I know some Windows configuration profiles missing in Intune portal, if there is any misunderstanding, feel free to let me know.
To clarify this issue, please check the following.
1.Please check the audit log to see if the configuration profiles were accidentally deleted or renamed by someone.
https://learn.microsoft.com/en-us/mem/intune/fundamentals/monitor-audit-logs
2.We can use Graph API or PowerShell to get all configuration profile to make sure it is not a display issue, and the profiles are actually there.
https://cloudinfra.net/3-ways-to-export-intune-device-configuration-profiles/
https://doitpshway.com/get-all-intune-policies-using-powershell-and-graph-api
Non-official, just for reference.
Please try above information, if there is any update, feel free to let me know.
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