Thanks for the suggestion Nick. I had compared both of my projects (one works and the other doesn't) and the source code looks the same but one project has all of the Glossary links broken.
I also noticed that when getting either project from source control only the broken one asks me to overwrite a writeable version of "eHlpDhtm.js". The file also shows up in the Baggage Files folder in the broken project but not in the working project.
I forgot to mention before that I am using RoboHelp 8.
Below is the code from the one not working:
<?xml version="1.0" encoding="utf-8" ?>
<!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>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="topic-check-list" content="First Draft" />
<meta name="topic-comment" content="Waiting for Appointments to be moved to .net" />
<meta name="generator" content="Adobe RoboHelp 8" />
<title>Counseling Tab</title>
<link rel="StyleSheet" href="../All Sheets.css" type="text/css" />
</head>
<body><script type="text/javascript" language="JavaScript1.2" src="..\eHlpDhtm.js"></script>
<h1>Counseling Tab</h1>
<p>The purpose of the Counseling tab is to allow the user to view specific
items related to the counseling session.</p>
 
<p>Please click on the following glossary terms for their definitions:</p>
<p style="margin-top: 0; margin-bottom: 0;"> </p>
<p style="margin-left: 40px;"><a class="glossterm" href="javascript:TextPopup(this)" id="HotSpot43003">Date Counseled</a><script type="text/javascript">//<![CDATA[
TextPopupInit('HotSpot43003', 'POPUP43003');
//]]></script><span class="glosstext" id="POPUP43003" style="display: none;"> The date in which the lead/client was counseled with the counselor.</span>
</p>
<p style="margin-left: 40px;"><a class="glossterm" href="javascript:TextPopup(this)" id="HotSpot43538">Appointment Specialist</a><script type="text/javascript">//<![CDATA[
TextPopupInit('HotSpot43538', 'POPUP43538');
//]]></script><span class="glosstext" id="POPUP43538" style="display: none;"> Allows the user to set the appointment specialist, who is the person that originally scheduled an appointment with the client. If an appointment is booked through Book New Appointment in the Client or Appointments menu bar or through the Activity section on the Client screen or Main Menu, the Appointment Specialist field is filled in automatically with the name of the user to whom the appointment is assigned. If more than one appointment is scheduled for the client with different users, the Appointment Specialist field will retain the name of the first user that scheduled an appointment.</span>
</p>
<p style="margin-left: 40px;"><a class="glossterm" href="javascript:TextPopup(this)" id="HotSpot52147">Appointment Outcome</a><script type="text/javascript">//<![CDATA[
TextPopupInit('HotSpot52147', 'POPUP52147');
//]]></script><span class="glosstext" id="POPUP52147" style="display: none;"> Select from the dropdown list the outcome of the first contact with the lead.</span>
</p>
</body>
</html>
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