Sorry to open a such an old thread, but I'm having some troubles with a very
similar situation as the one I previously described.

I ended up going with Rob's first suggestion - the Bundle has A.msi, B.msi,
C.msi, B.msp, and C.msp (B.msi and C.msi are not embedded and not included). 
So far we haven't been releasing patches for A (since it's fairly small it's
easier to just do major upgrades).

We've released several updates and are now on version 1.0.5.  1.0.5 was a
fairly large change, so we released it as a major update.

We now want to release a small patch to A (to bring it up to 1.0.6), and
leave B and C alone.  B and C add up to over 1GB of data (hence the reason
for the patches to being with), so we obviously don't want our users to have
to re-download a full update.

Everything I've tried to do has resulted in A being updated, and B and C
getting uninstalled.  Here is a pared down version of my wxs file:

<Wix xmlns="http://schemas.microsoft.com/wix/2006/wi";
     xmlns:bal="http://schemas.microsoft.com/wix/BalExtension";
     xmlns:util="http://schemas.microsoft.com/wix/UtilExtension";>
  <?define ProductVersion="1.0.6" ?>
  <?define ProductName="Product" ?>
  <?define UpgradeCode="UPGRADE_GUID" ?>
  <?define Manufacturer="Company" ?>
  
        <Bundle Name="$(var.ProductName)" Version="$(var.ProductVersion)"
Manufacturer="$(var.Manufacturer)" UpgradeCode="$(var.UpgradeCode)">
    <BootstrapperApplicationRef
Id="WixStandardBootstrapperApplication.RtfLicense" >
        <bal:WixStandardBootstrapperApplication
LicenseFile="$(var.AssetsPath)\License.rtf" SuppressOptionsUI="yes" />
    </BootstrapperApplicationRef>

    <Chain>
        <MsiPackage SourceFile="$(var.MsiPath)" DisplayInternalUI="no">
            <MsiProperty Name="INSTALLFOLDER" Value="[InstallFolder]" />
        </MsiPackage>
        <MsiPackage SourceFile="A.msi" DisplayInternalUI="no"
Compressed="no">
            <SlipstreamMsp Id="A_Patch" />
        </MsiPackage>
        <MsiPackage SourceFile="B.msi" DisplayInternalUI="no"
Compressed="no">
            <SlipstreamMsp Id="B_Patch" />
        </MsiPackage>
        <MspPackage Id="A_Patch" SourceFile="A_Patch.msp"
DisplayInternalUI="no" Compressed="yes" />
        <MspPackage Id="B_Patch" SourceFile="B_Patch.msp"
DisplayInternalUI="no" Compressed="yes" />
    </Chain>
        </Bundle>
</Wix>



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