I have the following code to modify the author base on WP:

add_action('init', 'modify_author_slug');
function modify_author_slug() {
    global $wp_rewrite;
    $wp_rewrite->author_base = 'user';
    $wp_rewrite->author_structure = '/' . $wp_rewrite->author_base . '/%author%';
}

add_filter('query_vars', 'user_query_vars');
function user_query_vars($vars) {
    $new_vars = array('user');
    $vars = $new_vars + $vars;
    return $vars;
}

function user_rewrite_rules( $wp_rewrite ) {
  $newrules = array();
  $new_rules['user/(\d*)$'] = 'index.php?author=$matches[1]';
  $wp_rewrite->rules = $new_rules + $wp_rewrite->rules;
}
add_filter('generate_rewrite_rules','user_rewrite_rules');

The profile works great when I go to mysite/user/whatever. But, when using the get_author_posts_url(get_current_user_id()) function it returns mysite/author/whatever

I saved the permalink structure multiple times, flushed cache and tried using other browsers. Always happens the same.

Any idea?

EDIT

I am using the following function as I can not redirect with the get_author_posts_url(), it is still the problem, but the below code gives more context and can be used as a workaround.

// Remove access to administration to users
function blockusers_init() {
    if ( is_admin() && !current_user_can('administrator') && !( defined('DOING_AJAX') && DOING_AJAX ) ) {
        $url = home_url() . '/user/' . get_the_author_meta( 'user_nicename', get_current_user_id() );
        wp_redirect($url);
        exit;
    }
}
add_action( 'init', 'blockusers_init' );