Easily scan a double sided document once for every side (just turn the paper stack) through the automatic document feeder and merge with this script these two pdfs to one.

duplexScanCreator.sh

#!/usr/bin/env bash

# Description:
# Easily scan a double sided document once for every side (just turn the paper stack)
# through the automatic document feeder and merge with this script these two pdfs to one.
# Arguments:
# 1) & 2) The paths to the two pdf files that should be combined
# 3) The pdf file name of the combined file
# Example:
# sh .\duplexScanCreator.sh .\DocScan1.pdf .\DocScan2.pdf .\DocScan.pdf

# Get page numbers
PAGE_NUMBER_1=$(pdfinfo $1 | grep Pages | awk '{print $2}')
PAGE_NUMBER_2=$(pdfinfo $2 | grep Pages | awk '{print $2}')

if [ "$PAGE_NUMBER_1" -eq "$PAGE_NUMBER_2" ]
then
	echo "The page numbers are equal"
else
	echo "The page numbers are not equal"
	exit 1
fi

# Create single pages out of the files
pdfseparate $1 a_%d.pdf
pdfseparate $2 b_%d.pdf

# Create an array in the correct order
ARRAY=()
for (( c=1; c<=$PAGE_NUMBER_1; c++ ))
do
	ARRAY+=("a_${c}.pdf")
	OTHER_NUMBER=$(($PAGE_NUMBER_1 + 1 - $c))
	ARRAY+=("b_${OTHER_NUMBER}.pdf")
done

pdfunite "${ARRAY[@]}" $3
echo "File was written: $3"

# Now remove the created files
ARRAY=()
for (( c=1; c<=$PAGE_NUMBER_1; c++ ))
do
	rm "a_${c}.pdf"
	rm "b_${c}.pdf"
done