A photoshop script to flatten hierarchy of layer groups without merging layers.

FlattenLayerHierarchy.js

// Extract layers (flatten layer hierarchy, without merging) and remove empty layers
// Notice: layer effects on groups are not concerened
#target photoshop

if (!app.documents.length) {
  alert('No document is opened', 'No document');
}
else {
  app.activeDocument.suspendHistory('Flatten Layer Hierarchy', 'processLayers()');
}

function processLayers()
{
  while (app.activeDocument.layerSets.length) {
    extractLayers(app.activeDocument);
  }
  removeEmptyLayers (app.activeDocument);
}

function extractLayers(doc)
{
  var toRemove = [];
  for (var i = doc.layerSets.length-1; i >= 0; i--) {
    //$.writeln(doc.layerSets[i].name);
    var parent = doc.layerSets[i];
    var children = parent.layers;
    var toMove = [];
    for (var j = 0; j < children.length; j++) {
      toMove.push(children[j]);
    }
    for (var j = 0; j < toMove.length; j++) {
      moveLayerToLayerSet(toMove[j].id, parent.id);
    }
    toRemove.push(parent);
  }
  for (var i = 0; i < toRemove.length; i++) {
    toRemove[i].remove();
  }
}

function moveLayerToLayerSet( fromID, toID ){  
  var desc = new ActionDescriptor();  
  var ref = new ActionReference();  
  ref.putIdentifier( charIDToTypeID('Lyr '), Number(fromID) );  
  desc.putReference( charIDToTypeID('null'), ref );  
  var ref2 = new ActionReference();  
  ref2.putIndex( charIDToTypeID('Lyr '), getLayerIndexByID(toID) );  
  desc.putReference( charIDToTypeID('T   '), ref2 );  
  desc.putBoolean( charIDToTypeID('Adjs'), false );  
  desc.putInteger( charIDToTypeID('Vrsn'), 5 );  
  try{  
    executeAction( charIDToTypeID('move'), desc, DialogModes.NO );  
  } catch(e) {
    alert(e);
  }  
}

function getLayerIndexByID(ID){
  var backgroundCounter = 0;
  if (app.activeDocument.artLayers.length) {
    backgroundCounter = activeDocument.artLayers[activeDocument.artLayers.length-1].isBackgroundLayer ? 1 : 0;
  }
  var ref = new ActionReference();  
  ref.putIdentifier( charIDToTypeID('Lyr '), ID );  
  return executeActionGet(ref).getInteger(charIDToTypeID( "ItmI" ))-backgroundCounter;   
}

function isEmptyLayer(layer) {
  if (layer.kind == LayerKind.TEXT) {
    if ("" == layer.textItem.contents) {
      return true;
    }
  }
  else {
    if (layer.bounds[2] == 0 && layer.bounds[3] == 0) {
      return true;
    }
  }
  return false;
}

function removeEmptyLayers(doc) {
  for (var i = doc.artLayers.length - 1; i >= 0; i--) {
    if (isEmptyLayer(doc.artLayers[i])) {
      if (app.activeDocument.layers.length > 1) { 
        doc.artLayers[i].remove();
      }
    }
  }
}