My question is directly linked to the thread Make Skim save PDF's with embedded notes by default
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.
Skim version 1.4.18 running on El Capitan