I had a similar problem for the past few days. Instead of
Request.GetOwinContext().Authentication.authenticationManager.SignOut();
Use ONE(and only one) of these:
Request.GetOwinContext().Authentication.SignOut();
Request.GetOwinContext().Authentication.SignOut(Microsoft.AspNet.Identity.DefaultAuthenticationTypes.ApplicationCookie);
HttpContext.Current.GetOwinContext().Authentication.SignOut(Microsoft.AspNet.Identity.DefaultAuthenticationTypes.ApplicationCookie);
This article explains why your cookies don’t get deleted: https://dzone.com/articles/catching-systemwebowin-cookie
I know my answer isn’t the most research-based, but to tell you the truth, I just couldn’t find WHY my provided code examples work for me. I just know that System.Web messes up Owins cookies if you do SignOut() another way.