Website goes down after uploading Master page - asp.net

My question is about Asp.Net website hosting on shared server. I have a website which has 1 master page and 4000 child pages, website is made in asp.net but pages are like static - I am not using any database in it. I simple create a child page from the master page, write the Title, Heading, Description & content. Website has 30,000 to 40,000 pageviews per day.
The issue is that: When I make any change in the master page, website went down for 3-4 hours. No issue with child page uploading - to upload the pages I use FileZilla(any number of child page can be uploaded and no Issue of website down).
I am using GoDaddy's Ultimate Windows Hosting plan
Here is my Master page code:
<%# Master Language="VB" AutoEventWireup="true" CodeFile="mpageR.master.vb" Inherits="mywebsite" %>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head runat="server">
<title></title>
<meta charset="UTF-8" />
<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<link rel="stylesheet" href="css/W3.css"/>
<link rel="stylesheet" href="css/style1.css"/>
<!-- START: Analytics-->
<!-- Analytics code-->
<script type="text/javascript">
...
</script>
<!-- END: Analytics Code-->
<asp:ContentPlaceHolder id="head" runat="server">
</asp:ContentPlaceHolder>
</head>
<body>
<!--Main Page Section-->
<form id="form1" runat="server">
<div class="w3-row">
<!--Header control (reading a file in this control to show header section)-->
<%# Register TagPrefix="uc" TagName="header_cntrl" Src="~/user-controls/header.ascx" %>
<uc:header_cntrl id="header_cntrl1" runat="server"/>
<!--End of Header-->
</div>
<div class="w3-row">
<!--main section-->
<div class="left-panel">
<!-- Left Nav Menu (reading file for left panel)-->
<%# Register TagPrefix="uc" TagName="LeftNavMenu" Src="~/plugins/LeftNavMenu.ascx" %>
<uc:LeftNavMenu id="LeftNavMenu" runat="server"/>
<!-- End of Left Nav Menu-->
</div>
<div class="main-panel">
<asp:ContentPlaceHolder id="ContentPlaceHolder1" runat="server">
</asp:ContentPlaceHolder>
</div>
<div class="right-panel">
<!-- Right Nav Menu (reading file for right section)-->
<%# Register TagPrefix="uc" TagName="RgtNavMenu" Src="~/plugins/RgtNavMenu.ascx" %>
<uc:RgtNavMenu id="RgtNavMenu" runat="server"/>
<!-- End of Right Nav Menu-->
</div>
</div>
<br />
<!--Footer control (reading file for footer)-->
<%# Register TagPrefix="uc" TagName="footer_cntrl" Src="~/user-controls/footer.ascx" %>
<uc:footer_cntrl id="footer_master" runat="server"/>
<!--End of Footer-->
</form>
<!--End of Main Page Section-->
</body>
</html>
Web.config file:
<?xml version="1.0"?>
<configuration>
<system.web>
<compilation debug="true" targetFramework="4.0">
</compilation>
<pages controlRenderingCompatibilityVersion="3.5" clientIDMode="AutoID"/>
<customErrors mode="On">
<error redirect="~/error.aspx" statusCode="404"/>
</customErrors>
</system.web>
<system.webServer>
<rewrite>
<rules>
<rule name="Redirect to WWW" stopProcessing="true">
<match url=".*" />
<conditions>
<add input="{HTTP_HOST}" pattern="^mywebsiye.com$" />
</conditions>
<action type="Redirect" url="https://www.mywebsite.com/{R:0}"
redirectType="Permanent" />
</rule>
</rules>
</rewrite>
</system.webServer>
</configuration>

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<h1>Upcoming Programs</h1>
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<p align="center">Long Programs | Workshops | Affiliates' & Other Workshops | Summer Programs & Special Events
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<%--<a name="long"><ipam:program_list id="idProgramList1" Type="Long" Time="Upcoming" runat="server" /></a>
<a name="workshops"><ipam:program_list id="idProgramList2" Type="Short" Time="Upcoming" runat="server" /></a>
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I use VS2008 and it doesn't come up in my intellisense either.
[Edit]
<%# Page Title="" Language="VB" MasterPageFile="~/MasterPage.master"
AutoEventWireup="false" CodeFile="test.aspx.vb" Inherits="accesscontrol_test" %>
<%# Register TagPrefix="IPAMControl" TagName="confirm_list" Src="Copy of nav.ascx" %>
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<hr size="1">
<p align="center"><a href="#long" >Long Programs</a></p>
Our upcoming programs include long programs, short programs (workshops), reunion
conferences, and summer programs. Click on the program title for detailed information.
<a name="long"><IPAMControl:confirm_list id="idconfirm_list" runat="server">
</IPAMControl:confirm_list></a>
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The above code works fine for me, try registering it at the top of the page like I did, then we can help pinpoint what's causing the issue. You'll obviously have to change the directives, but register it in the page and not the web config.
[Edit]
Try adding this to your web config in <pages><controls>
<add tagPrefix="IMAPControl" namespace="IMAP.Webmaster.Controls" assembly="IMAP.Webmaster" />

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