The process is in DocStore and it copies the files, so it does duplicate them. But once they're in the DocStorage folders after that process, the link in AR doesn't look to the SoftPDF folder anymore. So you shouldn't have the issue with windows accessing the large folder.

The question as to why the new invoices continue to be copied to the SOFTPDF folder after AR 9.3A and IN 9.3A are installed is one for Softrak Tech Support. I just noticed mine are also going to both places.