In many English dictionaries, "retraction" can mean either a disavowal/withdrawn endorsement, or to take back/withdraw.

Paper newspapers had no physical way of doing the latter without literally pulling every copy in existence, which would be impossible once it's been released (as you also pointed out). Because of that, you can't really infer the correct use of the term based off what they did. Furthermore, languages evolve, so even if that was the only "correct" use of the term back then does not mean it's also the only use today.

I'm happy to agree that none of this should be held up by a dispute over mere semantics. And I agree that languages evolve, and is used different but consistently by different communities at different times. But let me just note that since most scientific journals and some newspapers use "retract" to mean disavowal without textual removal, clearly describing whatever NPR and the NYTimes are doing requires an additional word (or at least a modifier). The term I've heard used sometimes, and which I think is clear, is "unpublish" (but this is not standardized).