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As indicated in the help topic for the Make VS.NET action
"It supports VC++.NET (managed and unmanaged), Visual C#, VB.NET, and J# .NET projects (other project types in a solution will be built, but the added features will not be performed)..."
Since a setup (.vdproj) file is just a text file, you could use the Replace in File action to set the version, something like this (you can copy and paste this step into VBP):
<step action='Replace in File' type='0'>
<FileIn>%VDPROJ_FILE%</FileIn>
<FileOut>%VDPROJ_FILE%</FileOut>
<Find>"ProductVersion"\s*=\s*"8:([[^"]]*)"</Find>
<Replace>"ProductVersion" = "8:%BUILD_NUM%"</Replace>
<indent type='3'>1</indent>
<name>Set Version</name>
</step>
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