Script for copying a jpeg and pasting it on another jpeg

I tweaked a script and I am almost there. It stacks 2 images and saves as a psd and moves on to the next 2 images. Is there a way to keep the stacked images in Photoshop while the script is still working on the other images?

// MAC Finder or WINDOWS Explorer  double click enabled   
#target photoshop  
app.bringToFront();  

// Variables  
var docRefSup = "";  
var docRefInf = "";  
var layerRef = "";  
var psd_Options  = new PhotoshopSaveOptions(); // [PhotoshopSaveOptions]   
psd_Options.layers  = true; // preserve layers  
psd_Options.embedColorProfile = true; // preserve color profile  
psd_Options.annotations = true; // preserve annotations  
psd_Options.alphaChannels = true; // preserve Alpha channels  
psd_Options.spotColors = true; // preserve Inks  

// Selection the INPUT folder and put the images in an Array  
var inputFolder = new Folder("/G/Images/2014-2015");
var inputFolder = inputFolder.selectDlg();
var outputFolder = Folder(inputFolder + "/../");  
// Create a directory as OUTPUT folder if it does not exist  
if (!outputFolder.exists) outputFolder.create();  
var fileList = inputFolder.getFiles(/\.(jpg|jpeg|png|psd|)$/i);  
// Main program  
for (var i= 0;i<fileList.length;i++)   
{  
    docRefSup = open(fileList);  
    docRefInf = open(fileList[i+1]);  
    
    var startRulerUnits = app.preferences.rulerUnits;
app.preferences.rulerUnits = Units.PIXELS; // tell ps to work with pixels
    
    app.activeDocument = app.documents[1];  
    layerRef = app.activeDocument.activeLayer.bounds; 
    app.activeDocument.selection.selectAll()
    app.activeDocument.selection.copy();
    var selectedRegion = Array(Array(layerRef[0].value,layerRef[1].value),Array(layerRef[2].value,layerRef[1].value),Array(layerRef[2].value,layerRef[ 3].value),Array(layerRef[0].value,layerRef[3].value));
    app.activeDocument = app.documents[0];
    app.activeDocument.selection.select(selectedRegion); 
    app.activeDocument.paste(true);  
    var fileName  = app.activeDocument.name;  
    // Save the combined file  
    
    app.activeDocument.saveAs(File(outputFolder + '/' + fileName), psd_Options, true );  
    app.activeDocument.close(SaveOptions.DONOTSAVECHANGES);  
    app.activeDocument.close(SaveOptions.DONOTSAVECHANGES);  
    i++;  
}
// Opens PPR Folder
var dir = Folder(inputFolder + "/../");  
var files = dir.openDlg('This is always the same folder?','',true);  
if( files !=null ){  
     for(var f = 0;f< files.length;f++){  
          open(files);  
     }  
}
// END