I just finished scanning some old two sided hand written notes into two pdf files. Specifically I created 'odd.odf' for odd numbered pages (e.g. page 1, 3, 5, ...), and 'even.pdf' for even numbered pages (e.g. page 2, 4, 6, ...). The below script takes these two files, and uses pdftk to merge them into a single 'result.pdf' document.

#
# Create directory, or clean it contents if it already exists 
#
rm -f ./result.pdf
mkdir -p mytmpdir
cd ./mytmpdir
rm -rf ./*

#
# Take the pdf with odd pages (1,3,5,etc) and split
# it into individual pages.
#
mkdir -p odd
cd odd
pdftk ../../odd.pdf burst
i=1;
for myfile in ./*.pdf
do
	newfile=$(printf "page_%04d.pdf" $i) 
	mv $myfile $newfile
	let i=i+2
done
cd ..

#
# Take the pdf with even pages (2,4,6,etc) and split
# it into individual pages.
#
mkdir -p even
cd even
pdftk ../../even.pdf burst
let i=2;
for myfile in ./*.pdf
do
	newfile=$(printf "page_%04d.pdf" $i) 
	mv $myfile $newfile
	let i=i+2
done
cd ..

#
# Create the final file result.pdf
#
mv -f odd/*.pdf .
mv -f even/*.pdf .
pdftk *.pdf cat output ../result.pdf