solution to easily embed skim notes doesn't work

My question is directly linked to the thread https://apple.stackexchange.com/questions/79429/make-skim-save-pdfs-with-embedded-notes-by-default/235387#235387 What if the proposed solution (https://apple.stackexchange.com/a/166794/180243) doesn't help? As in, I worked my way through all steps, but when I press command + s it still saves normally rather than embedded. I just found out I lost 200 hours of carefully made annotations, and I really want to avoid that from ever happening again. Please help. Skim version 1.4.18 running on El Capitan