Back in May, someone asked on the Adobe forum if there was a way to export 2 pdfs from InDesign at once, using different presets.

The answer was the following little script, which can be easily adapted to exported more than just 2 PDFs, using any existing PDF presets you like:

// BS"D 
// All rights reserved (c) 2015 by 
// Free to use and modify but do not delete this copyright attribution. 
// This script will export 2 pdfs of the current document 
// Choose the PDF presets by altering their names below 
// The second PDF gets a suffix added to its name. 
// Modify the line below beginning name2 = to change the suffix. 
// For more InDesign scripts: 
d = app.activeDocument; 
// Here you can choose the PDF preset 
preset1 = app.pdfExportPresets.itemByName("[High Quality Print]"); 
preset2 = app.pdfExportPresets.itemByName("[Smallest File Size]"); 
if (!(preset1.isValid && preset2.isValid)){ 
 alert("One of the presets does not exist. Please check spelling carefully."); 
if (d.saved){ 
 thePath = String(d.fullName).replace(/\..+$/, "") + ".pdf"; 
 thePath = String(new File(thePath).saveDlg()); 
 thePath = String((new File).saveDlg()); 
thePath = thePath.replace(/\.pdf$/, ""); 
name1 = thePath+".pdf"; 
// Here you can set the suffix at the end of the name 
name2 = thePath+"_xx.pdf"; 
d.exportFile(ExportFormat.PDF_TYPE, new File(name1), false, preset1); 
d.exportFile(ExportFormat.PDF_TYPE, new File(name2), false, preset2);