Nuget Update - Specify MSBuild configuration to target - visual-studio

Question

Is there a way to restrict the nuget update command to only update .proj references that match a particular condition? (Or a clever workaround to get to the desired outcome)
Scenario
I have a project file that brings in different references depending on the ${Configuration}
type. So, for example, if the ${configuration} matches ProjRef it will set certain external references as ProjectReferences. If the ${configuration} matches the standard Release or Debug it will set certain external references as References.
This works great until nuget is added to the mix. If I run a nuget update via command line it will modify the .proj file outside of the ${configuration} conditionals and, therefore, override them if the added lines come after the ${configuration} conditionals.
Example
Before Running Nuget Update
<ItemGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|AnyCPU' ">
<Reference Include="X">
<HintPath>path\1.2.2\X.dll</HintPath>
</ItemGroup>
<ItemGroup Condition=" '$(Configuration)|$(Platform)' == 'ProjRef|AnyCPU' ">
<ProjectReference Include="X.vbproj">
<Name>X</Name>
</ProjectReference>
</ItemGroup>
After Running Nuget Update:
<ItemGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|AnyCPU' ">
</ItemGroup>
<ItemGroup Condition=" '$(Configuration)|$(Platform)' == 'ProjRef|AnyCPU' ">
<ProjectReference Include="X.vbproj">
<Name>X</Name>
</ProjectReference>
</ItemGroup>
<ItemGroup>
<Reference Include="X">
<HintPath>path\1.2.3\X.dll</HintPath>
</ItemGroup>
Notice that the lines added by nuget update will override the configuration specific lines resulting in no project reference -- even if built using ProjRef configuration.