GPOADmin currently does not have any knowledge of pure Azure AD groups from within the GPOADmin console. This is why they are being removed when the policies are edited with GPOADmin. This is also why we cannot manage them in GPOADmin currently.
We have created an enhancement to improve the handling of pure Azure AD groups in Intune Policy assignments. The enhancement ID to be considered for inclusion in a future version of GPOADmin is 519803
ER 519803 - Add the ability to manage Azure AD only groups for assignments in Intune Policies.
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