I tried and reproduce the problem.I was follow the below steps.

1. I was installed new MSi version 1.0.0
2. I was implemented minor upgrade and MSI version is 1.1.0
3. Then I tried for major upgrade (version 4.1.0).

First 2 steps are working fine, but when i tried for 3 step its throw the
error.Also its not pass the directory ref to the custom action.

<DirectoryRef Id="INSTALLLOCATION">
    <Component Id="MicrosoftDataSchema"
Guid="AA67D22F-12E9-4034-BD7D-7210A43050BD">
      <File Id="Microsoft.Data.Schema.dll"
Source="$(var.SrcArchPath)Microsoft.Data.Schema.dll" KeyPath="yes"
Checksum="yes"/>
    </Component>
    <Component Id="MicrosoftDataSchemaScriptDom"
Guid="AA17D22F-22E9-4034-BD7D-7210A43050BD">
      <File Id="Microsoft.Data.Schema.ScriptDom.dll"
Source="$(var.SrcArchPath)Microsoft.Data.Schema.ScriptDom.dll" KeyPath="yes"
Checksum="yes"/>
    </Component>
    <Component Id="MicrosoftDataSchemaScriptDomSql"
Guid="AA67D22F-32E9-4034-BD7D-7210A43050BD">
      <File Id="Microsoft.Data.Schema.ScriptDom.Sql.dll"
Source="$(var.SrcArchPath)Microsoft.Data.Schema.ScriptDom.Sql.dll"
KeyPath="yes" Checksum="yes"/>
    </Component>
    <Component Id="MicrosoftDataSchemaSql"
Guid="AA67D22F-42E9-4034-BD7D-7210A43050BD">
      <File Id="Microsoft.Data.Schema.Sql.dll"
Source="$(var.SrcArchPath)Microsoft.Data.Schema.Sql.dll" KeyPath="yes"
Checksum="yes"/>
    </Component>
    <Component Id="Vsdbcmd" Guid="AA67D22F-52E9-4034-BD7D-7210A43050BD">
      <File Id="vsdbcmd.exe" Source="$(var.SrcArchPath)vsdbcmd.exe"
KeyPath="yes" Checksum="yes"/>
    </Component>
    <Component Id="VsdbcmdConfig"
Guid="AA67D22F-52E9-4034-BD7D-7210A43050BA">
      <File Id="vsdbcmd.exe.config"
Source="$(var.SrcArchPath)vsdbcmd.exe.config" KeyPath="yes" Checksum="yes"/>
    </Component>
  </DirectoryRef>
When my custom action run, the above reference should pass to the CA, its
not passed thats why its not installed.
Can you help me to fix the problem.

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