Complex sentence: The $4.6 million planned extension would have taken the trail to the Indigo Tunnel, but not through it, because an environmental impact study determined it houses the largest known bat refuge in Maryland.
Split into simpler sentences: The $4.6 million planned extension would have taken the trail to the Indigo Tunnel, but not through it for environmental reasons. An environmental impact study determined that the tunnel houses the largest known bat refuge in Maryland.