Let's say you want to place all the translated .resx files in a Translations folder, like this (note I have left the default and en versions in the root folder):

Then all you need to do is edit the MSBuild project file (from Visual Studio, right-click on the project node, 'Unload project', then 'Edit xxx.csproj'), and reconfigure each Resx file in this folder like this:

before:

  <ItemGroup>
    ...
    <EmbeddedResource Include="Resource1.en.resx" />
    <EmbeddedResource Include="Translations\Resource1.fr.resx" />
    <EmbeddedResource Include="Resource1.resx">
      <Generator>ResXFileCodeGenerator</Generator>
      <LastGenOutput>Resource1.Designer.cs</LastGenOutput>
    </EmbeddedResource>
    ...
  </ItemGroup>

after:

  <ItemGroup>
    ...
    <EmbeddedResource Include="Resource1.en.resx" />
    <EmbeddedResource Include="Translations\Resource1.fr.resx">
      <ManifestResourceName>$(TargetName).%(Filename)</ManifestResourceName> <!-- add this for all .resx files in a custom folder -->
    </EmbeddedResource>
    <EmbeddedResource Include="Resource1.resx">
      <Generator>ResXFileCodeGenerator</Generator>
      <LastGenOutput>Resource1.Designer.cs</LastGenOutput>
    </EmbeddedResource>
    ...
  </ItemGroup>

What it does is instruct underlying MSBuild tasks to use the manifest name you specificy instead of generating one automatically. The automatically generated one always uses the folder layout where the RESX resides in which is not what we want.

After compilation, the final satellite ConsoleApplication1.resources.dll file will be placed in the fr folder as usual, but its content will be the same as if the resx file was placed in the root folder.