@Lowe, Troy, Thanks for posting in Q&A.
According to your description, I know that you want to know why after deleting the settings related to app protection policy, the app still be applied to app protection policy.
Based on my researching, it is suggested that you see the log in the targeted device by entering about:intunehelp in Edge to check whether app protection policy is applied.
Moreover, please check whether conditional access policy is assigned to the user, if yes, the app will also receive the message that the application is being managed by Company policy.
However, if you do not want app to apply app protection policy, you can unassign it and the app will not apply app protection policy.
Thanks for your kind understanding.
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