Check and Uncheck all CheckBox for ASP.Net GridView inside UpdatePanel

Try this

    <asp:ScriptManager ID="ScriptManager1" runat="server">
    </asp:ScriptManager>
    <asp:UpdatePanel ID="up1" runat="server">
        <ContentTemplate>
            <asp:GridView ID="GridView1" runat="server" AutoGenerateColumns="false">
                <Columns>
                    <asp:TemplateField>
                        <HeaderTemplate>
                            <asp:CheckBox ID="chkAll" runat="server" AutoPostBack="true" OnCheckedChanged="OnCheckedChanged" />
                        </HeaderTemplate>
                        <ItemTemplate>
                            <asp:CheckBox ID="CheckBox1" runat="server" AutoPostBack="true" OnCheckedChanged="OnChildCheckedChanged" />
                        </ItemTemplate>
                    </asp:TemplateField>
                    <asp:BoundField DataField="Item" />
                    <asp:BoundField DataField="Price" />
                </Columns>
            </asp:GridView>
        </ContentTemplate>
    </asp:UpdatePanel>
    <hr />
    <asp:UpdatePanel ID="up2" runat="server">
        <ContentTemplate>
            <asp:GridView ID="GridView2" runat="server" AutoGenerateColumns="false">
                <Columns>
                    <asp:TemplateField>
                        <HeaderTemplate>
                            <asp:CheckBox ID="chkAll" runat="server" AutoPostBack="true" OnCheckedChanged="OnCheckedChanged" />
                        </HeaderTemplate>
                        <ItemTemplate>
                            <asp:CheckBox ID="CheckBox1" runat="server" AutoPostBack="true" OnCheckedChanged="OnChildCheckedChanged" />
                        </ItemTemplate>
                    </asp:TemplateField>
                    <asp:BoundField DataField="Item" />
                    <asp:BoundField DataField="Price" />
                </Columns>
            </asp:GridView>
        </ContentTemplate>
    </asp:UpdatePanel>

protected void Page_Load(object sender, EventArgs e)
{
    if (!IsPostBack)
    {
        DataTable dt = new DataTable();
        dt.Columns.AddRange(new DataColumn[2] { new DataColumn("Item"), new DataColumn("Price") });
        dt.Rows.Add("Shirt", 199);
        dt.Rows.Add("Football", 020);
        dt.Rows.Add("Shirt", 566);
        dt.Rows.Add("Disc", 099);
        dt.Rows.Add("Watch", 54);
        dt.Rows.Add("Clock", 890);
        GridView1.DataSource = dt;
        GridView1.DataBind();
        GridView2.DataSource = dt;
        GridView2.DataBind();
    }
}
protected void OnCheckedChanged(object sender, EventArgs e)
{
    CheckBox chk = (sender as CheckBox);
    GridView gv = chk.NamingContainer.Parent.Parent as GridView;
    foreach (GridViewRow row in gv.Rows)
    {
        if (row.RowType == DataControlRowType.DataRow)
        {
            (row.FindControl("CheckBox1") as CheckBox).Checked = chk.Checked;
        }
    }
}
protected void OnChildCheckedChanged(object sender, EventArgs e)
{
    CheckBox chk = (sender as CheckBox);
    GridView gv = chk.NamingContainer.Parent.Parent as GridView;
    bool isAllChecked = true;
    foreach (GridViewRow row in gv.Rows)
    {
        if (row.RowType == DataControlRowType.DataRow)
        {
            if (!(row.FindControl("CheckBox1") as CheckBox).Checked)
            {
                isAllChecked = false;
                break;
            }
        }
    }
    CheckBox chkAll = (gv.HeaderRow.FindControl("chkAll") as CheckBox);
    chkAll.Checked = isAllChecked;
}