So from what I get from this is that some third party cartridges actually use HP chips (presumably from reels of chips sold to a re-manufacturer of cartridges so HP can track down the re-manufacturer/batch if Joe has a printing quality problem, or whatever) and some just clone whatever chip they found first (I'm picturing thousands of printers all reporting that they have cartridge with SN#2477751135432 installed and it amuses me).
I've seen some pretty convincing fake cartridges in my time that hold themselves out to be genuine, brand new in box units. That said, the firmware had previously said "This cartridge has been previously used or is non-genuine" upon insertion and you could click okay to continue.
I haven't read specifically whether self-refilled, store-refilled or store-bought third-party cartridges were affected, or whether this was just for cartridges bought from the usual suspects (some ebay sellers, amazon vendors, ali*, etc). Working in a big box store, though, I haven't yet had customers complain about it, though, so with my tiny sample size, I'm going to theorize that is the case.