I have also tried a version using last modified dates..

<Message Text="Copying MyProject Config Files: $(ConfigFilesPath) - #@(ConfigContentFiles->Count()) files" Importance="high" />
        <Copy SourceFiles="@(ConfigContentFiles)" DestinationFiles="@(ConfigContentFiles->'$(MSBuildProjectDirectory)\config\%(RecursiveDir)%(Filename)%(Extension)')" SkipUnchangedFiles="true"
           Condition="%(Filename)!='' AND (!Exists('$(MSBuildProjectDirectory)\config\%(RecursiveDir)%(Filename)%(Extension)') OR $([System.DateTime]::Parse('%(ModifiedTime)').Ticks) > $([System.IO.File]::GetLastWriteTime('$(MSBuildProjectDirectory)\config\%(RecursiveDir)%(Filename)%(Extension)').Ticks))" />