I'm with Dave on this, It should have been a simple mater of using a transit and properly marking the "Shoreline", BUT if getting "them" to redo it right is not an option...the only thing that comes to mind is to drive anchors into the ground above the shoreline and run cables down into the water that would be attached to plastic/wood composite boards that would create a shelf so that rocks could be piled up out of the water and over the exposed liner without sliding to the bottom.
This sounds expensive and labor intensive, but that's all I got for you unless some sort of vegetation could be talked into growing above the exposed liner and gracefully drape down to the water.
