Script: Export as EPS, AI, PNG all in the same folder

Give this a try. Seems to work on my end.. But i'm only guessing as to the actual contents and formatting of your own folder structure and such so i can't be certain this will work on your end.

//Script Name: i have no idea what to call it.. any ideas?
//Script Author: Adobe Support Forum User danielj15115761
//Adobe Discussion Post: https://community.adobe.com/t5/illustrator/script-export-as-eps-ai-png-all-in-the-same-folder/td-p/12135881
//Script Edited by: Dilliam Wowling
	//Email: illustrator.dev.pro@gmail.com
	//github: github.com/wdjsdev
	//paypal: https://www.paypal.com/paypalme/illustratordev

#target Illustrator
function main()
{

	//logic container vvvv


	//function for saving the doc
	//into each necessary format.
	function saveDoc(doc)
	{
		var fn = doc.fullName.toString();
		var docName = fn.substring(fn.lastIndexOf("/")+1,fn.length).replace(/\.[aipdf]{2,3}/i,"");
		var savePath = fn.substring(0,fn.lastIndexOf("/")+1);

		var saveFile;
		var ext;
		var opts;

		//save the ai file:
		ext = ".ai";
		doc.saveAs(File(savePath + docName + ext));

		//save the eps
		opts = new EPSSaveOptions();
		ext = ".eps";
		doc.saveAs(File(savePath + docName + ext),opts);

		ext = ".jpg"
		doc.exportFile(File(savePath + docName + ext),ExportType.JPEG);

		ext = ".png"
		doc.exportFile(File(savePath + docName + ext),ExportType.PNG24);
		

	}

	//generic function for identifying a layer by name
	//essentially this replaces the native getByName()
	//method that causes a runtime error if the layer
	//doesn't exist. this will just return undefined
	//if the layer doesn't exist.
	function findSpecificLayer(parent,layerName,crit)
	{
		var result,layers;

		if(parent.typename === "Layer" || parent.typename === "Document")
		{
			layers = parent.layers;	
		}
		else if(parent.typename === "Layers")
		{
			layers = parent;
		}
		
		for(var x=0,len=layers.length;x<len && !result;x++)
		{
			if(crit && crit === "any" && layers[x].name.toLowerCase().indexOf(layerName.toLowerCase())>-1)
			{
				result = layers[x];
			}
			else if(layers[x].name.toLowerCase() === layerName.toLowerCase())
			{
				result = layers[x];
			}
		}
		return result;
	}


	//depth first recursive search
	//no max depth. pushes all ai or eps files
	//anywhere inside the given folder to global
	//allFiles array for processing.
	function scanSubFolders(tFolder)
	{
		var files = tFolder.getFiles();

		for(var f=0;f<files.length;f++)
		{
			if(files[f] instanceof File && aiEpsRegex.test(files[f].name))
			{
				allFiles.push(files[f]);
			}
			else if(files[f] instanceof Folder)
			{
				scanSubFolders(files[f]);
			}
		}
	}


	//logic container ^^^^




	//procedure vvvv


	var sFolders = [];
	var allFiles = [];

	//ask the user for a folder to process
	var inputFolder = Folder.selectDialog("Select a folder to process")
	if (inputFolder === null)
	{
		return undefined;
	}


	var aiEpsRegex = /\.(ai|eps)$/i;

	//get the files from the given folder and its subfolders
	scanSubFolders(inputFolder);
	if(!allFiles.length === 0)
	{
		alert("No files found to process.");
		return undefined;
	}


	var docsToClose = [];
	for (var i = allFiles.length - 1; i >= 0; i--)
	{
		app.open(allFiles[i]);
		var doc = app.activeDocument;
		var docLayers = doc.layers;
		var bgLayer = findSpecificLayer(docLayers,"background");
		if(bgLayer && docLayers.length > 1)
		{
			bgLayer.remove();
		}

		saveDoc(doc);
		docsToClose.push(doc);
	}


	for(var d=docsToClose.length-1;d>=0;d--)
	{
		docsToClose[d].close(SaveChanges.DONTSAVECHANGES);
	}

	//procedure ^^^^
}

main()

Script 1:

function main() {

        var inputFolder = Folder.selectDialog("Select a folder to process")
         if (inputFolder != null){
        var fileandfolderAr = scanSubFolders(inputFolder, /\.(ai|eps)$/i);
        var fileList = fileandfolderAr[0];
        }
        for (var i = fileList.length-1; i >= 0; i--) {
        app.open(fileList[i]);
        var doc = app.activeDocument;
        try {
            var docLayers = doc.layers;
            var n = docLayers.length;
            docLayers[n-1].visible = true;
            docLayers[n-1].locked = false; 
            docLayers[n-1].remove();
            doc.save();
            doc.close(SaveOptions.NO);
        } catch (e) {

        }
    }
}

main()

function scanSubFolders(tFolder, myAI) {
var sFolders = [];
var allFiles = [];
sFolders[0] = tFolder;

for (var j = 0; j < sFolders.length; j++) {
var procFiles = sFolders[j].getFiles();

for (var i = 0; i < procFiles.length; i++) {
if (procFiles[i] instanceof File) {
if(myAI == undefined) {
allFiles.push(procFiles);
}

if (procFiles[i].fullName.search(myAI) != -1) {
allFiles.push(procFiles[i]);
  }
}

else if (procFiles[i] instanceof Folder) {
sFolders.push(procFiles[i]);
scanSubFolders(procFiles[i], myAI);
    }
  }
}
return [allFiles, sFolders];
}

Script 2:

function main() {
    var folder = Folder(Folder.desktop + "/New Files");
    if (!folder.exists)
        folder.create();
    var fileList = File.openDialog("Selest Files", "All:*.eps*", true);
    for (var i = fileList.length-1; i >= 0; i--) {
        app.open(fileList[i]);
        var doc = app.activeDocument;
        try {
            //var _backgroudLayer = doc.layers.getByName('background');
            //_backgroudLayer.remove();
            var pI= doc.pathItems;
            var n = pI.length; 
            pI[n-1].selected;
            pI[n-1].remove();
            var fileName = doc.name;
            doc.saveAs(File(folder + "/" + fileName));
            doc.close(SaveOptions.DONOTSAVECHANGES);
        } catch (e) {

        }
    }
}

main()