How to: auto stack smart objects into single file

Here is a slightly refined version of the original script, this version will name the SO Stack layers after the original document to aid in layer identification:

var baseDoc = app.activeDocument;
var baseName = app.activeDocument.name.replace(/\.[^\.]+$/, ''); // Base Doc Name RegEx
app.activeDocument.activeLayer.name = baseName;
baseDoc.duplicate('SO Stack');
baseDoc.close(SaveOptions.DONOTSAVECHANGES);

// Duplicate single SO layer to SO Stack doc
for (var i = 0; i < app.documents.length; i++) {
    app.activeDocument = app.documents[i];
    displayDialogs = DialogModes.NO;

    var docName = app.activeDocument.name.replace(/\.[^\.]+$/, ''); // Source Doc Name RegEx
    duplicate(docName, 5); // Source Doc for Duplicate Layer Rename
    function duplicate(name2, version) {
        var c2t = function (s) {
            return app.charIDToTypeID(s);
        };
    
        var s2t = function (s) {
            return app.stringIDToTypeID(s);
        };
    
        var descriptor = new ActionDescriptor();
        var list = new ActionList();
        var reference = new ActionReference();
        var reference2 = new ActionReference();
    
        reference.putEnumerated(s2t("layer"), s2t("ordinal"), s2t("targetEnum"));
        descriptor.putReference(c2t("null"), reference);
        reference2.putName(s2t("document"), "SO Stack"); // Target Doc for Duplicate Layer
        descriptor.putReference(s2t("to"), reference2);
        descriptor.putString(s2t("name"), name2);
        descriptor.putInteger(s2t("version"), version);
        list.putInteger(3);
        descriptor.putList(s2t("ID"), list);
        executeAction(s2t("duplicate"), descriptor, DialogModes.NO);
    }

};

// Remove the extra layer (yes this is hack to work around the poor coding :)
app.activeDocument.layers[0].remove();

// Close all open files that are not named 'SO Stack'
var docs = app.documents;
for (var i = docs.length - 1; i >= 0; i--) {
    if (docs[i].name.indexOf('SO Stack') < 0) {
        docs[i].close();
    }
}

P.S. You could graft this code onto the end of the script to alphabetically sort the layers:

https://gist.github.com/vladocar/1628874

var layers = activeDocument.layers;
	var layersArray = [];
	var len = layers.length;
	


	// store all layers in an array
	for (var i = 0; i < len; i++) {
		layersArray.push(layers[i]);
	}

	// sort layer top to bottom
	layersArray.sort();

	for (i = 0; i < len; i++) {
		layersArray[i].move(layers[i], ElementPlacement.PLACEBEFORE);
    }

The following script is not that clean/pretty, but it does work.

Open all single layer smart object files that you wish to stack, then run this script. It is assumed that all files are the same pixel dimensions, colour mode/space and resolution.

The result will be a single open image, with each separate input image being a smart object layer. Layer names and sort order leave something to be desired...

var baseDoc = app.activeDocument;
baseDoc.duplicate('SO Stack');
var soStack = app.activeDocument;
baseDoc.close();

// Duplicate single SO layer to soStack doc
for (var i = 0; i < app.documents.length; i++) {
    app.activeDocument = app.documents[i];
    displayDialogs = DialogModes.NO;
    app.activeDocument.layers[0].duplicate(soStack);
};

// Remove the extra layer (yes this is hack to work around the poor coding :)
app.activeDocument.layers[0].remove();

// Close all open files that are not named 'SO Stack'
var docs = app.documents;
for(var i = docs.length - 1; i >= 0; i--){
   if(docs[i].name.indexOf('SO Stack') < 0){
      docs[i].close();
   }
}

https://prepression.blogspot.com/2017/11/downloading-and-installing-adobe-scripts.html

That was my first thought r-bin – however it does not work with open files that contain a single SO layer, which is what I understand the OP is dealing with:

I just tried with no open files, and they were all silently skipped.

You can use Layer > Duplicate Layer to dupe a copy of Doc A to Doc B, retaining the smart object from Doc A.

An action can fully automate the task if you always have the same number of files to combine. An action could semi-automate some of the manual steps of this task if the open document count varies... however, a script would be ideal.