Combines PDF files and adds white pages in between to allow double-sided printing without mixing documents. Requires a blank.pdf file.

combinepdf.sh

#! /bin/bash

if [ -z "$1" ]; then
    echo "Specify which folder contains the PDFs"
    exit 1
fi

OUTFILE=combined_$1.pdf

if command -v convert >/dev/null 2>&1; then
	convert xc:none -page A4 blank.pdf
elif command -v pdflatex >/dev/null 2>&1; then
	pdflatex -jobname 'blank' "\documentclass[a4paper]{article}\usepackage{geometry}\begin{document}\null\end{document}" >/dev/null 2>&1
	rm -f blank.aux
	rm -f blank.log
elif ! [[ -e 'blank.pdf' ]]; then
	echo "Could not find 'convert' or 'pdflatex'; manually create an empty PDF called blank.pdf"
	exit 1
fi

first=true
i=$OUTFILE
o=$(mktemp)
for f in $1/*.pdf
do
	if $first; then
		first=false
		args=("$f")
	else
		args=($i "$f")
	fi
	c=$(pdftk "$f" dump_data output | grep -i NumberOfPages | sed s/NumberOfPages:\ //)
	if [ $(($c%2)) = 1 ]; then
		args+=(blank.pdf)
	fi
	pdftk "${args[@]}" cat output $o
	t=$i
	i=$o
	o=$t
done
if [ -f $o ]; then
	rm $o
fi
mv $i $OUTFILE

Thanks for your contribution. It helped me to get an idea to where i need to go.
The problem here is that your script is running out of memory after a certain amount of iterations (in my case 700+ PDFs with 6 pages on average) because you concatenate each newly created pdf with each next pdf recursively instead of extending first the odd paged PDFs and then merging all at once at the end.
This can be done in a performant and elegant one-liner assuming you have a blank.pdf already available. (See: https://superuser.com/questions/1442122/supressing-duplex-for-single-pages-in-pdf)
pdftk $(for i in *.pdf; do echo $i; pdftk $i dump_data | perl -ne 'print "/path/to/blank.pdf\n" if (m/NumberOfPages: (\d+)/ && $1 % 2 == 1)'; done) cat output merged.pdf