In Public/Mapping/StandardAtlasBuilderMapping[Fx].xml:

     <Elements Name="Decal_Custom_LogoUmbralChoir_01">

      <Id>31</Id>

      <Left>768</Left>

      <Top>1792</Top>

      <Width>256</Width>

      <Height>256</Height>

      <Source>Assets/HxFx/Textures/Atlas_Decal/Decal_Custom_LogoUmbralChoir_01.tga</Source>

    </Elements>

     <Elements Name="Decal_Custom_LogoUmbralChoir_01">

      <Id>32</Id>

      <Left>1024</Left>

      <Top>1792</Top>

      <Width>256</Width>

      <Height>256</Height>

      <Source>Assets/HxFx/Textures/Atlas_Decal/Decal_Custom_LogoHissho_01.tga</Source>

    </Elements>

The XML that adds the Hissho Logo is misconfigured to override the Umbral Choir Decal, resulting in no Decal appearing on either faction's ships.