A new update has been released addressing the issues with the Codex for some players.
The Repair Codex option in Preferences will unlock everything your save should have by the end of the current content. In order to avoid potential spoilers, please only use this option if you have problems with your Codex and you have already finished the latest content.
We also recommend using this option only with your save file loaded, this will ensure the Repair function be able to read your save and unlock entries appropriately based on your choices.