I was in the same predicament. After avoiding it for a while, I realized that it might be worth it to make a regular practice of reviewing old non-atomic notes and, using something like Note Composer, extracting the key headings or blocks that can exist as useful independent ideas for future use, leaving behind the embed. I actually use a Templater script that adds the source text into a source heading, leaving behind the embed to that. I appreciate your feature request Note Composer: links to blocks and headers should be updated when extracting , and understand the friction and/or limitations of doing this en masse.
At the very least, by doing this, these underlying ideas wouldn’t be hiding behind a note name that cannot fully explain the contents. And using MOCs and properties, you can feel less of a need to have everything linked perfectly because you will have decent clumps. Not sure this answer is anything you haven’t already considered, but just wanted to share my experience because I was thinking the same things.
The review process becomes part of the new normal. I have yet to fully catch up and almost can’t imagine what it will be like when and if I ever do. Good luck!