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I've create app-only context for Sharepoint Online using GetAzureADAppOnlyAuthenticatedContext method (SharePointPnPCoreOnline.3.5.1901). Azure app has 'Have full control of all site collections' application permission for Office 365 SharePoint Online API.

However checked out files are not visible despite Draft Item Security in Versioning Settings. The current value of versioning settings: Who should see draft items in this library? - Any user who can read items.

How to make these documents visible for app-only authenticated context without taking ownership?

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The permission scopes defined in the manifests are not intuitive in that they don't bubble all the way down. So, "full control of all site collections" doesn't mean exactly that. There's a permission scope that allows you to manage lists or read list items. You'll have to find the exact one you need for your situation and apply it.

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