I've solved this particular issue.  The solution was to move the WebConfigCmp 
into a separate sub-feature like below.  My next step will be to partition 
AppliationWebFiles components into separate <Fragments> so that I can deliver 
them selectively in Small Patches which is my ultimate goal.

    <Feature Id="Complete" Title="Middle Tier" Level="1" Display="expand" 
ConfigurableDirectory="INSTALLLOCATION">

      <Feature Id="WebSiteConfiguration" Title=" Website Configuration" 
Description="The website configuration" Level="1">
        <ComponentGroupRef Id="WebIssConfiguration" />
        <ComponentRef Id="WebConfigCmp" />
        <ComponentRef Id="ProgramMenuDir" />
      </Feature>

      <Feature Id="WebFiles" Title="Website Content" Description="The website 
content" Level="1">
        <ComponentGroupRef Id="ApplicationWebFiles" />
      </Feature>

    </Feature>



From: kjk129 [via Windows Installer XML (WiX) toolset] 
[mailto:ml-node+s687559n7597506...@n2.nabble.com]
Sent: Monday, October 27, 2014 9:12 AM
To: Kurtis J. Kyle
Subject: Re: Patch installing component with Not Installed condition

I have a very similar problem.  I've created a single Feature install that 
includes a large set of files to install along with some other components such 
as one to install and modify the web.config.  My new install works fine, 
however my Patch is trying to re-install the component for the web.config and 
it fails.  My Patch file WXS explicitly names only 2 components to install. ( 
neither the web.config )

I tried adding the NOT INSTALLED condition, but that did not change things.  My 
understanding is that my Patch file should take care of explicitly determining 
which files to install.  I've used TORCH/PRYO and Product.wixout files from the 
new install folder and the patch folder to produce this MSP patch.   I've 
successfully implemented this with the more simplistic examples such as "WiX 
Patch Example Product".

Any thoughts on where I am going wrong?

                <DirectoryRef Id="MYWEBFOLDER">

                        <Component Id="WebConfigCmp" 
Guid="B356E039-6930-4703-BAC9-8B07CA2B413C" >
        <Condition>

<![CDATA[NOT Installed]]>

</Condition>

                                <File Id="WebConfigFile" KeyPath="yes" 
Source="$(var.SourceDirectory)\web.config" Vital="yes" />
        <util:XmlFile Id="ModifyRolePassword"
                         Action="setValue"
                         Permanent="yes"
                         
ElementPath="/configuration/appSettings/add[\[]@key='RolePassword'[\]]"
                         Name="value"
                         File="[#WebConfigFile]"
                         Value="[DB_APP_ROLE_PWD]"
                         SelectionLanguage="XSLPattern"
                         Sequence="1" />

                        </Component>
                </DirectoryRef>


My patch WXS looks like this:

<?xml version="1.0" encoding="UTF-8"?>
<Wix 
xmlns="http://schemas.microsoft.com/wix/2006/wi";><http://schemas.microsoft.com/wix/2006/wi%22%3e>
  <Patch
      AllowRemoval="yes"
      Manufacturer="xyz"
      MoreInfoURL="http://www.usa.com/";<http://www.usa.com/%22>
      DisplayName="HF1"
      Description="HF1"
      Classification="Hotfix"
        >
    <Media Id="5000" Cabinet="RTM.cab">
      <PatchBaseline Id="RTM"/>
    </Media>
    <PatchFamilyRef Id="PatchFamily"/>
  </Patch>
  <Fragment>
    <PatchFamily Id='PatchFamily' Version='2.0.0.000' Supersede='yes'>
      <PropertyRef Id="ProductVersion"/>
      <ComponentRef Id="comp_8533AA6FF41A43C6969A14985BB1DD1C" />
      <ComponentRef Id="WebUI.dll" />
    </PatchFamily>
  </Fragment>
</Wix>
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