There would be two ways to mark only the parent link as active.

1. With jQuery

The advantage of this is that it will be compatible with any back end platform.

<script>
    $(document).ready(function () {
        var current = location.pathname;
        console.log(current);
        $("#navigation-menu a").each(function () {
            var $this = $(this);
            var link = $this.attr('href');
            console.log(link);

            // Remove the query string parameters by finding their starting position
            var indexOfQueryString = link.lastIndexOf("?");
            link = link.substring(0, indexOfQueryString);

            if (link.endsWith(current)) {
                console.log("matched");
                if ($this.parent().parent().hasClass('.dropdown-menu')) {
                    var parentLink = $this.closest('.dropdown');
                    console.log("Setting parent link as active:", parentLink);
                    // Find the closest parent link and add active class
                    parentLink.addClass('active');
                } else {
                    console.log("Setting link as active: ", $this.parent());
                    $this.parent().addClass('active');
                }
            }
        });
    });
</script>

In this case, as you have mentioned you encountered problems with ?Agent being present in link – this is what we refer to as query string parameters, which we can safely remove by searching for the unencoded question mark. This is already considered in the solution.

2. With ASP.NET MVC

Doing this in the back end would be more robust and should JavaScript be disabled by the user, this functionality will still work in your website. The disadvantage though, as you might have guessed, is that it is platform-dependent.

There are many ways of going about this. For your specific use-case, as your dropdown links are related to the parent by area, I have adapted another SO answer to cover your specific use-case:

public static string IsSelected(this HtmlHelper html, string area = "", string cssClass = "active")
{
    ViewContext viewContext = html.ViewContext;
    RouteValueDictionary routeValues = viewContext.RouteData.Values;
    string currentArea = routeValues["area"] as string;

    return area.Equals(currentArea) ? cssClass : String.Empty;
}

Then use it this way:

<ul class="sidebar-menu" id="navigation-menu">
    <li><a asp-area="" asp-controller="Home" asp-action="Index" class="nav-link"><i class="fas fa-home"></i><span>Home
                Page</span></a></li>
    <li class="nav-item dropdown @Html.IsSelected(area: "Configuration")">
        <a href="#" class="nav-link has-dropdown"><i class="fas fa-cog"></i><span>Configuration</span></a>
        <ul class="dropdown-menu">
            <li><a asp-area="Configuration" asp-controller="AccountCodes" asp-action="Index" class="nav-link">Account
                    Codes</a></li>
            <li><a asp-area="Configuration" asp-controller="Branches" asp-action="Index" class="nav-link">Branches</a>
            </li>
        </ul>
    </li>
    <li class="nav-item dropdown  @Html.IsSelected(area: "Directory")">
        <a href="#" class="nav-link has-dropdown"><i class="fas fa-person-booth"></i><span>Directory</span></a>
        <ul class="dropdown-menu">
            <li><a asp-area="Directory" asp-controller="Users" asp-action="Index" asp-route-Role="Administrator"
                    class="nav-link">Administrators</a></li>
            <li><a asp-area="Directory" asp-controller="Users" asp-action="Index" asp-route-Role="Manager"
                    class="nav-link">Managers</a></li>
            <li><a asp-area="Directory" asp-controller="Users" asp-action="Index" asp-route-Role="Agent"
                    class="nav-link">Agents</a></li>
        </ul>
    </li>
</ul>

Would this benefit you, please make sure to upvote the other linked answer as well.