in your project file in reference use an MSBUILD conditional
<Reference
Include="SomeAssembly86, Version=0.85.5.452, Culture=neutral, PublicKeyToken=41b332442f1101cc, processorArchitecture=MSIL"
Condition=" '$(Platform)' == 'AnyCPU' ">
<SpecificVersion>False</SpecificVersion>
<HintPath>....DependenciesSomeAssembly.dll</HintPath>
<Private>False</Private>
</Reference>
<Reference
Include="SomeOtherAssembly, Version=0.85.5.999, Culture=neutral, PublicKeyToken=41b332442f1101cc, processorArchitecture=MSIL"
Condition=" '$(Platform)' == 'x64' ">
<SpecificVersion>False</SpecificVersion>
<HintPath>....DependenciesSomeOtherAssembly.dll</HintPath>
<Private>False</Private>
</Reference>
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