Export mutations with several different layers

Hi sebastianp39925710,

Give the below code a try for your needs.

var doc = app.activeDocument;
var myFolder = doc.filePath;

export_preset = app.pdfExportPresets.itemByName("[High Quality Print]");

if (!(export_preset.isValid)){ 
    alert('The PDF export preset does not exist.'); 
    exit(); 
   }

function myGetVisibleLayers(){
 var myVisibleLayers = new Array;
  for (var i = 0; i < doc.layers.length; i++){
   if (doc.layers[i].visible == true) {   
    myVisibleLayers.push(doc.layers[i].index);
      }
   }
      return myVisibleLayers;
  }

 //Layers Manager Dialog/////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////

  var layerNames = [];

   for (var i = 0; i < doc.layers.length; i++) {
   layerNames.push(doc.layers[i].name);
   }
   var myW = new Window ("dialog", "Layers Manager"), 
   layerGroup = myW.add("group");
   layerGroup.alignChildren = "row";
   var columns = myW.add("group"); columns.spacing=20;
   
   layerGroup.add ('statictext', [-55,28,200, 43], "Select Base Layer(s)");
   var base = columns.add ("listbox", [30, 0, 275, 300] , layerNames, {multiselect: true});
   base.revealItem (doc.layers.length -i/1);
   var selectedBase = []; 
   for (var i = 0; i < base.items.length; i++){selectedBase[0] = base.items[i];}
   base.selection = selectedBase; 

   layerGroup.add ('statictext', [365, 28,603,43], "Select Version Layer(s)");   
   var versions = columns.add ("listbox", [30, 0, 275, 300] , layerNames, {multiselect: true});
   versions.revealItem (doc.layers.length -i/1);   
   var selected = []; 
   for (var i = 0; i < versions.items.length-1; i++){selected[i] = versions.items[i];}
   versions.selection = selected;

   var btn = myW.add("group");
   btn.orientation = "row";
   btn.alignment = ["right", "top"];
   var cancelBtn = btn.add ("button", undefined, "Cancel", {name:"Cancel"});
   var okBtn = btn.add ("button", undefined, "OK", {name:"OK"});
   
   var myResult = myW.show()   
   if(myResult == 1){  
   main();  
   }  
   else if (myResult== 2){  
   exit(0);  
   }  
   function main(){ 

///pdf /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////

   if (base.selection == null){
  alert ('Error!\nNo base layer was selected for pdf Output. Please try again.') 
  exit();
  }
  else if (versions.selection == null){
  alert ('Error!\nNo version layers(s) were selected for pdf Output. Please try again.')
  exit();
  }
 var lookup = {};
 for (var j in versions.selection) {lookup[versions.selection[j]] = versions.selection[j];}
 for (var i in base.selection) {
 if (typeof lookup[base.selection[i]] != 'undefined'){
 alert('The layer "'+ [base.selection[i]] + '" cannot be both a base and version layer.\nPlease try again.');
 exit ();
 break;
 } 
 }

 var myVisibleLayers = myGetVisibleLayers();
      
  doc.layers.everyItem().visible = false;

  for (var i = 0; i < base.selection.length; i++){
  var myBase = base.selection[i].index;

  doc.layers[myBase].visible =  true; 
  }

  for (var i = 0; i < versions.selection.length; i++){
  var myVersion = versions.selection[i].index;

  var my_layer = doc.layers[myVersion].name;

  doc.layers[myVersion].visible = true;
  
  app.pdfExportPreferences.pageRange = PageRange.ALL_PAGES

  doc.exportFile(ExportFormat.PDF_TYPE, File(myFolder +'/'+ my_layer + ".pdf"), false, export_preset);

  doc.layers[myVersion].visible = false;
}
  doc.layers.everyItem().visible = false;

  for (var i = 0; i < myVisibleLayers.length; i++){  
    var myLayers = myVisibleLayers[i];
    doc.layers[myLayers].visible =  true; 
    }
    alert('Done Exporting the selected Layers to a PDF!');
}

Regards,

Mike