This is a quick and (very dirty) python script that will export all of your remarkable notebooks to PDF files, and outputs them with the correct path based on the collection they're store in on the tablet.
You'll need to edit the script to set the notebook path directory and the output pdf path correctly, but it shouldn't be too hard to follow.
You'll need to compile https://github.com/rorycl/rm2pdf, as this script uses the binary and template pdf from there.