A wizard did it.I don’t buy the premise that it makes sense for only the final wish to be reversed. Yes, they were in the post-wish universe, but that was still also the universe of all the other wishes too. On top of that, Anya lost her powers back in the original universe as well as the wish one. She lost ALL her powers.
Or The Hellmouth. It exerts a force that drags certain people towards it. It is the reason that Buffy is always within spitting distance of numerous threats to the world. She didn't end up there by chance. It took a wish aimed at Buffy to get her away and she still turns up. All of the main cast are still knocking about in the new reality. After the point the old reality appears to be restored events are mentioned that we haven't seen and many you'd think significant never mentioned again. Spike's sire changes for example. Any changes outside of that main group wouldn't be apparent either. .