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>

</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";>
  <Patch 
      AllowRemoval="yes" 
      Manufacturer="xyz" 
      MoreInfoURL="http://www.usa.com/";
      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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