By default, the controls use embedded resources rather than external script files.  This means that modifying the script file doesn't actually do anything until you tell the control to use it.  Each control has a JavaScriptFileName property, which can be used to point it to a specific script file.  There's also a javascriptDirectory attribute which can be set in the web.config file to force all controls to use scripts in a special directory.  If you want to customize your scripts here's what I recommend you do.

1) copy the scripts folder you referenced above into your project

2) modify the web.config to add the infragistics tag handler and tag, and specify the directory name and relative path where the scripts are (likely ~/scripts/)

Here is a link for modifying the web.config file:

http://devcenter.infragistics.com/Support/KnowledgeBaseArticle.Aspx?ArticleID=6158

I am assuming by the name of the script file that you are using the UltraWebMenu that was retired in 2011 Volume 1.  If I am correct, you would set the JavaScriptFileName property to change the script file.

If I am incorrect and you are using the WebDataMenu, then you would need to tell the ScripManager to load the modified script file after telling it to load all dependent scripts.  For example:

<asp:ScriptManager ID="WebScriptManager1" runat="server">
    <Scripts>
        <asp:ScriptReference
            Name="Infragistics.Web.UI.Scripts.0_igControlMain.js"
            Assembly="Infragistics45.Web.v18.1, Version=18.1.20181.48, Culture=neutral, PublicKeyToken=7dd5c3163f2cd0cb" />
        <asp:ScriptReference
            Name="Infragistics.Web.UI.Scripts.1_igControlMainClientBinding.js"
            Assembly="Infragistics45.Web.v18.1, Version=18.1.20181.48, Culture=neutral, PublicKeyToken=7dd5c3163f2cd0cb" />
        <asp:ScriptReference
            Name="Infragistics.Web.UI.Scripts.2_igCollections.js"
            Assembly="Infragistics45.Web.v18.1, Version=18.1.20181.48, Culture=neutral, PublicKeyToken=7dd5c3163f2cd0cb" />
        <asp:ScriptReference
            Name="Infragistics.Web.UI.Scripts.3_igUIBehaviors.js"
            Assembly="Infragistics45.Web.v18.1, Version=18.1.20181.48, Culture=neutral, PublicKeyToken=7dd5c3163f2cd0cb" />
        <asp:ScriptReference
            Name="Infragistics.Web.UI.Scripts.4_igEnums.js"
            Assembly="Infragistics45.Web.v18.1, Version=18.1.20181.48, Culture=neutral, PublicKeyToken=7dd5c3163f2cd0cb" />
        <asp:ScriptReference
            Name="Infragistics.Web.UI.Scripts.5_igObjects.js"
            Assembly="Infragistics45.Web.v18.1, Version=18.1.20181.48, Culture=neutral, PublicKeyToken=7dd5c3163f2cd0cb" />
        <asp:ScriptReference
            Name="Infragistics.Web.UI.Scripts.6_igObjectsClientBinding.js"
            Assembly="Infragistics45.Web.v18.1, Version=18.1.20181.48, Culture=neutral, PublicKeyToken=7dd5c3163f2cd0cb" />
        <asp:ScriptReference
            Name="Infragistics.Web.UI.Scripts.7_igClientStateManager.js"
            Assembly="Infragistics45.Web.v18.1, Version=18.1.20181.48, Culture=neutral, PublicKeyToken=7dd5c3163f2cd0cb" />
        <asp:ScriptReference
            Name="Infragistics.Web.UI.Scripts.8_igCallback.js"
            Assembly="Infragistics45.Web.v18.1, Version=18.1.20181.48, Culture=neutral, PublicKeyToken=7dd5c3163f2cd0cb" />
        <asp:ScriptReference
            Name="Infragistics.Web.UI.Scripts.9_igPropertyManagers.js"
            Assembly="Infragistics45.Web.v18.1, Version=18.1.20181.48, Culture=neutral, PublicKeyToken=7dd5c3163f2cd0cb" />
        <asp:ScriptReference
            Name="Infragistics.Web.UI.NavigationControls.WebDataMenu.js.igDataMenuItem.js"
            Assembly="Infragistics45.Web.v18.1, Version=18.1.20181.48, Culture=neutral, PublicKeyToken=7dd5c3163f2cd0cb" />
        <asp:ScriptReference
            Name="Infragistics.Web.UI.NavigationControls.WebDataMenu.js.igWebDataMenu.js"
            Assembly="Infragistics45.Web.v18.1, Version=18.1.20181.48, Culture=neutral, PublicKeyToken=7dd5c3163f2cd0cb"
            Path="Scripts/igWebDataMenu.js" />
    </Scripts>
</asp:ScriptManager>

Its urgent!! someone from Infragistics team please respond on this.