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How can I convert pdf files with embedded files to files without these attachments and this in bulk (ie 100 at a time)?
This might be possible with programming, but for 100 files this would not save any time (as it would surely take days to get the programming working). So, open, delete attachments, SAVE AS (not just SAVE), close, repeat.
Also, to speed up the process, consider using watched folders.
Look at the second half of this page, you might get some insight https://helpx.adobe.com/ie/acrobat/using/creating-pdfs-acrobat-distiller.html