Merge two PDFs scanned from a double sided print, front.pdf and reverse.pdf. The reverse.pdf side is scanned in the reverse order to the front.

Extract images from multiple PDFs. The Poppler toolset provides pdfimages.

mkdir -p images/front
mkdir -p images/reverse
pdfimages -p -all front.pdf  images/front/
pdfimages -p -all reverse.pdf  images/reverse/

Rename by odd page numbers in same order.

cd images/front
i=1; for f in `ls -1 -- *.jpg | sort` ; do mv -- "$f" p-$i.jpg; i=$[$i + 2]; done   
mv * ..

Rename to even page numbers, reversing.

cd images/reverse
n_files=$(ls -1 -- *.jpg | wc -l)
i=$[$n_files*2] ; for f in `ls -1 -- *.jpg | sort` ; do  mv -- "$f" p-$i.jpg; i=$[$i - 2]; done
mv * ..

Create PDF from images. Using https://imagemagick.org/ or the fork http://www.graphicsmagick.org/

cd images/
convert `ls -1 p-*.jpg |  sort -n -t '-' -k 2` foo.pdf

No need for tools like PDFSam…