It makes sense not to grant items removed from the game, what they need to do is "scrub" the codex to remove those. Better than having to scrub N number of accounts with a codex that doesn't exists.
Also, for a codex they mean to fix and you can get later, well, more work for us to go back to get them but ok. The ones you really need are those tied to a quest of some kind that you wont be able to repeat later to get. That said, I believe there is one tied to a quest in Voss that they reset the quest so it can be repeated if you have done it before, so go figure.
I still can't understand why this is of such low interest to them. We need to step up the reports so that the issue goes up on priority. As a developer and manager, I would have made the responsibility of the programmers to make sure the codex changes get done as changes are made to the planets/quests. Or at least reported to a QA team for update. To me shows very little organization at BW.