I’ve found a solution to this problem.

Basically I add claim with admin username, if this claim exists, I know that impersonation is happening. When admin wants to stop impersonation, system retrieves original username for the claims, deletes old impersonated-cookie and creates a new cookie for the admin:

[AuthenticateAdmin] // <- make sure this endpoint is only available to admins
public async Task ImpersonateUserAsync(string userName)
{
    var context = HttpContext.Current;

    var originalUsername = context.User.Identity.Name;

    var impersonatedUser = await userManager.FindByNameAsync(userName);

    var impersonatedIdentity = await userManager.CreateIdentityAsync(impersonatedUser, DefaultAuthenticationTypes.ApplicationCookie);
    impersonatedIdentity.AddClaim(new Claim("UserImpersonation", "true"));
    impersonatedIdentity.AddClaim(new Claim("OriginalUsername", originalUsername));

    var authenticationManager = context.GetOwinContext().Authentication;
    authenticationManager.SignOut(DefaultAuthenticationTypes.ApplicationCookie);
    authenticationManager.SignIn(new AuthenticationProperties() { IsPersistent = false }, impersonatedIdentity);
}

More information is in my blog-post: User impersonation with ASP.Net Identity 2.

User Impersonation in Asp.Net Core

Upd July 2017: this topic is quite popular, so I’ve looked into user impersonation in Core and principles are very similar with updated API. Here is how to impersonate:

    [Authorize(Roles = "Admin")] // <-- Make sure only admins can access this 
    public async Task<IActionResult> ImpersonateUser(String userId)
    {
        var currentUserId = User.GetUserId();

        var impersonatedUser = await _userManager.FindByIdAsync(userId);

        var userPrincipal = await _signInManager.CreateUserPrincipalAsync(impersonatedUser);

        userPrincipal.Identities.First().AddClaim(new Claim("OriginalUserId", currentUserId));
        userPrincipal.Identities.First().AddClaim(new Claim("IsImpersonating", "true"));

        // sign out the current user
        await _signInManager.SignOutAsync();

        // If you use asp.net core 1.0
        await HttpContext.Authentication.SignInAsync(cookieOptions.ApplicationCookieAuthenticationScheme, userPrincipal);
        // If you use asp.net core 2.0 (the line above is deprecated)
        await HttpContext.SignInAsync(cookieOptions.ApplicationCookieAuthenticationScheme, userPrincipal);

        return RedirectToAction("Index", "Home");
    }

This is how to stop impersonation:

    [Authorize(Roles = "Admin")] // <-- Make sure only admins can access this 
    public async Task<IActionResult> StopImpersonation()
    {
        if (!User.IsImpersonating())
        {
            throw new Exception("You are not impersonating now. Can't stop impersonation");
        }

        var originalUserId = User.FindFirst("OriginalUserId").Value;

        var originalUser = await _userManager.FindByIdAsync(originalUserId);

        await _signInManager.SignOutAsync();

        await _signInManager.SignInAsync(originalUser, isPersistent: true);

        return RedirectToAction("Index", "Home");
    }

Full explanation in my blog: http://tech.trailmax.info/2017/07/user-impersonation-in-asp-net-core/
Full code sample on GitHub: https://github.com/trailmax/AspNetCoreImpersonation