I stopped using free NetFabb - both stand alone and on the MS Azure site) months ago and switched to 3D Builder exclusively. I've never had a problem with saving my corrected and simplified files at STL files. Maybe you have to be running native Windows 10 for this - which I do.
3MF file support has now been added in Simplify3D Version 4.0. You can import a 3MF file by dragging it into the application or clicking on the Import button and selecting the file. Hopefully this helps for any programs that may be using this new file format!