Hello! I have inherited this project with a WiX installer, and am required to make this version usefully upgrade the previous one! My problem comes in replacing the database files with new versions. No, the problem is not that they are locked, I can replace them manually, and in fact now ONE of them is replaced, while the other is not. Please, please tell me what I'm doing wrong here. I've tried several other solutions (including registry keys as KeyPath instead of CompanionFile) but nothing is quite working.

Here is (most of) the code of the .WXS file:

<Product Id='$(var.ProductCode)'
    UpgradeCode='$(var.UpgradeCode)'
    Name="Pathways"
    Version='$(var.ProductVersion)'
    Manufacturer='$(var.Manufacturer)'
    Language='1033'>


    <Package Id="*" 
     Description="Pathways Directory Software"
     InstallerVersion="301"
     Compressed="yes" />

    <WixVariable Id="WixUILicenseRtf" Value="License.rtf" />
    <Media Id="1" Cabinet="Pathways.cab" EmbedCab="yes" />

    <Upgrade Id="$(var.UpgradeCode)">
        <UpgradeVersion
    OnlyDetect="no"  
    Maximum="$(var.ProductVersion)"
    IncludeMaximum="no"
    Language="1033"
    Property="OLDAPPFOUND"
   />
        <UpgradeVersion
    Minimum="$(var.ProductVersion)"
    IncludeMinimum="yes"
    OnlyDetect="no"
    Language="1033"
    Property="NEWAPPFOUND"
   />
    </Upgrade>

    <Property Id="ALLUSERS">2</Property>

    <!-- directories -->
    <Directory Id="TARGETDIR" Name="SourceDir">

        <!-- program files directory -->
        <Directory Id="ProgramFilesFolder">
            <Directory Id="INSTALLDIR" Name="Pathways"/>
        </Directory>

        <!-- application data directory -->
        <Directory Id="CommonAppDataFolder" Name="CommonAppData">
            <Directory Id="CommonAppDataPathways" Name="Pathways" />
        </Directory>

        <!-- start menu program directory -->
        <Directory Id="ProgramMenuFolder">
            <Directory Id="ProgramsMenuPathwaysFolder" Name="Pathways" />
        </Directory>

        <!-- desktop directory -->
        <Directory Id="DesktopFolder" />

    </Directory>

    <Icon Id="PathwaysIcon" SourceFile="\\Fileserver\Release\Pathways\Latest\Release\Pathways.exe" />

    <!-- components in the reference to the install directory -->
    <DirectoryRef Id="INSTALLDIR">
        <Component Id="Application" Guid="EEE4EB55-A515-4872-A4A5-06D6AB4A06A6">
            <File Id="pathwaysExe" Name="Pathways.exe" DiskId="1" Source="\\Fileserver\Release\Pathways\Latest\Release\Pathways.exe" Vital="yes" KeyPath="yes" Assembly=".net" AssemblyApplication="pathwaysExe" AssemblyManifest="pathwaysExe">
                <!--<netfx:NativeImage Id="ngen_Pathways.exe" Platform="32bit" Priority="2"/> -->
            </File>

            <File Id="pathwaysChm" Name="Pathways.chm" DiskId="1" Source="\\fileserver\Release\Pathways\Dependencies\Pathways.chm" />

            <File Id="publicKeyXml" ShortName="RSAPUBLI.XML" Name="RSAPublicKey.xml" DiskId="1" Source="\\fileserver\Release\Pathways\Dependencies\RSAPublicKey.xml" Vital="yes" />
            <File Id="staticListsXml" ShortName="STATICLI.XML" Name="StaticLists.xml" DiskId="1" Source="\\fileserver\Release\Pathways\Dependencies\StaticLists.xml" Vital="yes" />

            <File Id="axInteropMapPointDll" ShortName="AXMPOINT.DLL" Name="AxInterop.MapPoint.dll" DiskId="1" Source="\\fileserver\Release\Pathways\Dependencies\AxInterop.MapPoint.dll" Vital="yes" />
            <File Id="interopMapPointDll" ShortName="INMPOINT.DLL" Name="Interop.MapPoint.dll" DiskId="1" Source="\\fileserver\Release\Pathways\Dependencies\Interop.MapPoint.dll" Vital="yes" />
            <File Id="mapPointDll" ShortName="MAPPOINT.DLL" Name="MapPoint.dll" DiskId="1" Source="\\fileserver\Release\Pathways\Dependencies\Interop.MapPoint.dll" Vital="yes" />

            <File Id="devExpressData63Dll" ShortName="DAAT63.DLL" Name="DevExpress.Data.v6.3.dll" DiskId="1" Source="\\fileserver\Release\Pathways\Dependencies\DevExpress.Data.v6.3.dll" Vital="yes" />
            <File Id="devExpressUtils63Dll" ShortName="UTILS63.DLL" Name="DevExpress.Utils.v6.3.dll" DiskId="1" Source="\\fileserver\Release\Pathways\Dependencies\DevExpress.Utils.v6.3.dll" Vital="yes" />
            <File Id="devExpressXtraBars63Dll" ShortName="BARS63.DLL" Name="DevExpress.XtraBars.v6.3.dll" DiskId="1" Source="\\fileserver\Release\Pathways\Dependencies\DevExpress.XtraBars.v6.3.dll" Vital="yes" />
            <File Id="devExpressXtraNavBar63Dll" ShortName="NAVBAR63.DLL" Name="DevExpress.XtraNavBar.v6.3.dll" DiskId="1" Source="\\fileserver\Release\Pathways\Dependencies\DevExpress.XtraNavBar.v6.3.dll" Vital="yes" />
            <File Id="devExpressXtraCharts63Dll" ShortName="CHARTS63.DLL" Name="DevExpress.XtraCharts.v6.3.dll" DiskId="1" Source="\\fileserver\Release\Pathways\Dependencies\DevExpress.XtraCharts.v6.3.dll" Vital="yes" />
            <File Id="devExpressXtraEditors63Dll" ShortName="EDITOR63.DLL" Name="DevExpress.XtraEditors.v6.3.dll" DiskId="1" Source="\\fileserver\Release\Pathways\Dependencies\DevExpress.XtraEditors.v6.3.dll" Vital="yes" />
            <File Id="devExpressXtraPrinting63Dll" ShortName="PRINT63.DLL" Name="DevExpress.XtraPrinting.v6.3.dll" DiskId="1" Source="\\fileserver\Release\Pathways\Dependencies\DevExpress.XtraPrinting.v6.3.dll" Vital="yes" />
            <File Id="devExpressXtraReports63Dll" ShortName="REPORT63.DLL" Name="DevExpress.XtraReports.v6.3.dll" DiskId="1" Source="\\fileserver\Release\Pathways\Dependencies\DevExpress.XtraReports.v6.3.dll" Vital="yes" />
            <File Id="devExpressXtraRichTextEdit63Dll" ShortName="RICHTE63.DLL" Name="DevExpress.XtraRichTextEdit.v6.3.dll" DiskId="1" Source="\\fileserver\Release\Pathways\Dependencies\DevExpress.XtraRichTextEdit.v6.3.dll" Vital="yes" />

            <RegistryValue Id="PathwaysInstallDir" Root="HKLM" Key="Software\Tribal Data Resources\Pathways" Name="InstallDir" Action="write" Type="string" Value="[INSTALLDIR]" />
        </Component>

    </DirectoryRef>

    <!-- application data components -->
    <DirectoryRef Id="CommonAppDataPathways">

        <Component Id="CommonAppDataPathwaysFolderComponent" Guid="087C6F14-E87E-4B57-A7FA-C03FC8488E0D">
            <CreateFolder>
                <Permission User="Everyone" GenericAll="yes" />
            </CreateFolder>

            <RemoveFolder Id="CommonAppDataPathways" On="uninstall" />
            <!-- <RegistryValue Root="HKCU" Key="Software\TDR\Pathways" Name="installed" Type="integer" Value="1" KeyPath="yes" />-->

        </Component>

        <Component Id="Settings" Guid="A3513208-4F12-4496-B609-197812B4A953" NeverOverwrite="yes">
            <File Id="settingsXml" KeyPath="yes" ShortName="SETTINGS.XML" Name="Settings.xml" DiskId="1" Source="\\fileserver\Release\Pathways\Dependencies\Settings\settings.xml" Vital="yes" />   
        </Component>


        <Component Id="Database" Guid="1D8756EF-FD6C-49BC-8400-299492E8C65D" >
            <!-- <RegistryValue Root="HKLM" Key="Software\TDR\Pathways\Database" Name="installed" Type="integer" Value="1" KeyPath="yes" /> -->
            <File Id="pathwaysMdf" Name="Pathways.mdf" DiskId="1" Source="\\fileserver\Shared\Databases\Pathways\SystemDBs\Pathways.mdf" CompanionFile="pathwaysExe" Vital="yes"/>
            <File Id="pathwaysLdf" Name="Pathways_log.ldf" DiskId="1" Source="\\fileserver\Shared\Databases\Pathways\SystemDBs\Pathways.ldf" CompanionFile="pathwaysExe" Vital="yes"/>

        </Component>



        <!--
   <Component Id="MDF" Guid="FFB7CE02-B592-4c44-A315-99CF4828E3D9" >
    <File Id="pathwaysMdf" KeyPath="yes" Name="Pathways.mdf" DiskId="1" Source="\\fileserver\Shared\Databases\Pathways\SystemDBs\Pathways.mdf" />
   </Component>

   <Component Id="LDF" Guid="9E4E3DCA-A067-47f4-9905-4AD5C35A8025" >
    <File Id="pathwaysLdf" KeyPath="yes" Name="Pathways_log.ldf" DiskId="1" Source="\\fileserver\Shared\Databases\Pathways\SystemDBs\Pathways.ldf" />
   </Component>
   -->
    </DirectoryRef>

    <!-- shortcut components -->
    <DirectoryRef Id="DesktopFolder">
        <Component Id="DesktopShortcutComponent" Guid="1BF412BA-9C6B-460D-80ED-8388AC66703F">
            <Shortcut Id="DesktopShortcut"
        Target="[INSTALLDIR]Pathways.exe"
        Name="Pathways"
        Description="Pathways Tribal Directory"
        Icon="PathwaysIcon"
        Show="normal"
        WorkingDirectory="INSTALLDIR" />
            <RegistryValue Root="HKCU" Key="Software\TDR\Pathways" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        </Component>
    </DirectoryRef>

    <DirectoryRef Id ="ProgramsMenuPathwaysFolder">
        <Component Id="ProgramsMenuShortcutComponent" Guid="83A18245-4C22-4CDC-94E0-B480F80A407D">
            <Shortcut Id="ProgramsMenuShortcut" Target="[INSTALLDIR]Pathways.exe" Name="Pathways" Icon="PathwaysIcon" Show="normal" WorkingDirectory="INSTALLDIR" />
            <RemoveFolder Id="ProgramsMenuPathwaysFolder" On="uninstall"/>
            <RegistryValue Root="HKCU" Key="Software\TDR\Pathways" Name="installed" Type="integer" Value="1" KeyPath="yes"/>
        </Component>
    </DirectoryRef>


    <Feature Id="App" Title="Pathways Application" Level="1" Description="Pathways software" Display="expand" ConfigurableDirectory="INSTALLDIR" Absent="disallow" AllowAdvertise="no" InstallDefault="local">
        <ComponentRef Id="Application" />
        <ComponentRef Id="CommonAppDataPathwaysFolderComponent" />
        <ComponentRef Id="Settings"/>
        <ComponentRef Id="ProgramsMenuShortcutComponent" />
        <Feature Id="Shortcuts" Title="Desktop Shortcut" Level="1" Absent="allow" AllowAdvertise="no" InstallDefault="local">
            <ComponentRef Id="DesktopShortcutComponent" />
        </Feature>
    </Feature>


    <Feature Id="Data" Title="Database" Level="1" Absent="allow" AllowAdvertise="no" InstallDefault="local">
        <ComponentRef Id="Database" />
    </Feature>

    <UIRef Id ="WixUI_FeatureTree"/>
    <UIRef Id="WixUI_ErrorProgressText"/>

    <UI>
        <Error Id="2000">There is a later version of this program installed.</Error>
    </UI>

    <CustomAction Id="NewerVersionDetected" Error="2000" />

    <InstallExecuteSequence>
        <RemoveExistingProducts After="InstallFinalize"/>
    </InstallExecuteSequence>

</Product>

Running this installer attempting the upgrade from the previous version ALMOST WORKS. The file that is giving me trouble is the one called "PathwaysMdf". Even though it's Component code is EXACTLY the same as the PathwaysLdf file, that file is replaced, while the MDF is NOT. You can see, commented out, some of the other things I've attempted, some from suggestions on stackoverflow.

The entire log file from running the upgrade is located at: http://pastebin.com/ppjhq6Wi

THANK YOU! Joshua