One strategy I thought of is to use a single markdown file like the Hamster system [1] and alphabetize the sections; then I print this file and take handwritten notes onto the print out; then when the diff is large enough, I update the markdown file, print it again, and repeat. The main disadvantage is needing to reprint the full file for what could be small changes. To address that I have considered putting a page return between each letter of the alphabet, so each section starts on a new page.
Do you have any strategies to effectively synchronise paper with digital notes?
[1] https://github.com/slowernews/hamster-system