Try removing and re-adding and/or refreshing the connection to OneNote from within the Flow Connections page. 
You can do so by clicking the ellipsis (...) for the OneNote connection (red circle), and then selecting Switch Account to re-login, or to Delete to completely remove the connector (red box). If you choose to Delete the connector, you would simply re-add it as you normally would.
Then, in your Flow, click the ellipsis (...) for the OneNote step or steps (red circle), and verify that you have the correct account selected under the My connections heading.
Finally, if you are still having issues, insure once more that the account(s) that you are trying to use within the Flow have full read/write access to the SharePoint team site(s) where the OneNote notebook(s) is.
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