After many calls and chats with Hexagon support, there is still no proper way of saving PDF and Excel files automatically (by checking the folder contents and increasing the index). PDFs prompt for save location now and then, excel files are often saved twice, sometimes with wrong index and sometimes half an hour after I ran the measurement routine the last time, suddenly 20 empty excel files are added to the folder.
Instead of asking me to check or change things, why doesn't PC-DMIS come with a proper update to fix this. Apparently the way they coded this way of saving to PDF and Excel is not robust at all.
Customer support service by UserEcho