(Using ASP.NET Identity 2.1, Microsoft.Owin.Security.Facebook 3.0.1 in a Web API project)
From here: https://developers.facebook.com/docs/facebook-login/login-flow-f
I had the same issue when I wanted to ensure the user had accepted all my permissions. As you probably know this can be detected by calling the /me/permissions url.
So I eventually solved it by simply deleting my app from the user's account.
You can do so by doing a DELETE request on the /me/permissions URL as documented here.
This will remove all permissions you requested from the user, so next time you try authenticating him through Facebook, the prompt appears again.