What
Quetzzz says is correct. The codex entries are added at the moment the "Codex Updated" notification is shown and as such the state is stored in the save file. Retro-actively editing entries only has an effect on new playthroughs.
I've used
You must be registered to see the links
for the codex and kinda regretting the choice exactly for this reason. It would be easier to store everything in a separate file and only store the locked/unlocked state for each entry. It's similar to how the scene gallery is set up and how I would handle it in a new game.