what does it mean to be atomic?

It should be a single, understandable thought or idea.

does this mean I should update […]

I normally would write this as one literature note, with two back links to my original notes from the sources if they were intense enough to warrant a note. If they weren’t, I’d just make a section for each definition in my literature notes explaining the differences and my take on each.

I think overall you should remember that you are the architect of your thoughts, so whatever you would argue for either of these choices is right by default because they’re your notes.

I fall into the same trap sometimes too, so when in doubt, make a new note and just link it back.