how to impersonate the user with httpclient in netcore?

Are you able to debug and see if the required cookies are being passed to the API and what exactly is failing? The cookie path must be set to say "/" to enable all paths to see that cookie.

Alternatives

If the API is internal then can you use BasicAuthentication, passing plain user/pwd as header? A better approach however is to use JWT.

I wont be able to provide code example, but theoretically this situation calls for the use of JWT (JSON web Token) based authorization, if possible.  The ideal case is separating auth server from resource servers (something like single signon). See this for example

http://bitoftech.net/2014/09/24/decouple-owin-authorization-server-resource-server-oauth-2-0-web-api/

However, even in the case of having the API and MVC together, you can just copy Request's "Bearer" (or "Token") header into the HttpClient and let the API authenticate that JWT. A simple google search will provide explanations like

http://hamidmosalla.com/2017/10/19/policy-based-authorization-using-asp-net-core-2-and-json-web-token-jwt/

This may however require your client (if using Angular/Other for example) to be aware of JWT based authentication. ASP.NET core also allows you to use multiple Authentication schemes for different parts of the app, so for example the API part may require JWT but for the rest whatever is already in place can work.

I hope this gives you some pointers ..

Thanks for you pointers. The will look at the articles and come back asap.

To Illustrate the issue.

HttpContext.Request.Cookies = 6 cookies

I Instantiate a new HttpClient with a new Cookie Container > CookieCount = 0

I make the API Call . HttpClient Cookie Container Count = 1

HttpContext.Request.Cookies = 6 Cookies not 7

I current see no way to automatically pass the cookies from Request.Cookies to Cookie Container and vice versa.