From the PDFsam forum: It appears that PDFsam currently cannot flatten a PDF file. Could this feature be added to the next version? This would add a lot of value to PDFsam. ..... In case "flattening" ...

PDF Flatten Linux script to flatten mark-ups added to .pdf files by editors such as Okular, LibreOffice Draw or Adobe Acrobat via Nautilus or other file managers. If you are trying to redact sections ...

In most cases, this will flatten the PDF file. • In the PDF file, use the "save as" command to save the tax form as an Adobe PostScript file (which has the suffix ".ps").