"Save As" Action adds "copy"

Perhaps this script is what you want. It should save a flat jpeg file over the  jpeg file you opened into Photoshop and  want to save overs after adding layers.  The document open in Photoshop will still be layered after the document has been saved as a flat jpeg file overwriting the opened jpeg file. The script save jpeg quality 10 file. My 79 year old eyes can not see  the differences between quality 10 and 12 and  quality10 file size is much smaller. You can easily change the 10 to 12 in the SaveAsJpeg.jsx file if you want a larger file..

try {
	var tmp = app.activeDocument.fullName.name;
    ftype = decodeURI(tmp.substring(tmp.lastIndexOf("."),)).toLowerCase();
	if (ftype==".nef" || ftype==".cr2" || ftype==".crw" || ftype==".dcs" || ftype==".raf" || ftype==".arw" || ftype==".orf") { throw "error1"; }
	fname = decodeURI(tmp.substring(0, tmp.lastIndexOf(".")));
	SaveAsJPEG(activeDocument.path + "/" + fname, 10);
}
catch(e) {alert("Document has not been save yet")}

function SaveAsJPEG(saveFile, jpegQuality){
	var doc = activeDocument;
	jpgSaveOptions = new JPEGSaveOptions();
	jpgSaveOptions.embedColorProfile = true;
	jpgSaveOptions.formatOptions = FormatOptions.STANDARDBASELINE;
	jpgSaveOptions.matte = MatteType.NONE;
	jpgSaveOptions.quality = jpegQuality;
	activeDocument.saveAs(File(saveFile+".jpg"), jpgSaveOptions, true,Extension.LOWERCASE);
}

For some reason when you record an action and use Save As and use the File Type pull-down and select Jpeg then click save. You get a pop up dialog stating the file exist do you want to replace it. When you click yes the Files is replaces there is no copy.  However the Action records no file name in the Action step but adds "With Copy". 

When you use the Action. The actions saves a  file named  "DocumentName copy.jpg".   If you do not want the File Name to have that " copy" suffix you have to rename the save file after deleting the existing file without the copy or you can write a Photoshop Script to do the save as jpeg without the copy suffix and use that script in your action in place of the Photoshop step "Save As".  Adobe most likely recorded the action With Copy so the step require user interaction so the action could be batched.  If the file exist the step would need to open the Save As UI pop up Dialog asking it you want to replace the file. When you record the action perhaps if you change the save to folder location you will  not get the With Copy recorded in the action step.    NO that does not work I change the save to folder to the desktop but as soon as I use the file type pull down ans select Jpeg Photoshop checks the Save as Copy option in the save as dialog  and grays it out so you can not remove the With Copy. It is forced on you only get the replace option dialog when  you  are using Photoshop UI.

Write the script it will not take many lines of javascript code.