As much as I like figuring stuff out from an in-universe perspective (Watsonian), I think you guys need to take a step back and think like a Doyalist (author/reader perspective).
A Doyalist would be asking, what would make for a better story?
And honestly, a lot of the theories in this thread... would not make a good story.
Some key facts to consider:
Proven Guilty came out ages ago. Think about what that means. We've all moved on, and meaningless details have mostly been forgotten. It would be incredibly boring to have something like, say, "Remember 10 years ago? That person who had the idea of tracking Molly through her mother's blood....wasn't Murphy at all!!!! (It was actually Mab).
Reader reaction would just be, "Oh. Huh."
Same thing with Ace. Ace is done. No one cares about Ace. Hell, people barely cared about Ace when he came back in Cold Days. I don't even remember if he's dead, that's how irrelevant Ace is. Imagine if we discovered that, 10 years ago... Ace almost hurt Harry with his car!!! (He didn't, though).
The problem is all the little inconsistencies in PG aren't actually important right now. If they're not important, they're not satisfying to read about.
And there's no way to MAKE them important, in the here and now- those books are done with, enemies defeated, everyone's moved on.
Luckily... we have a wizard, and Jim is chatty. Consider the following:
- Proven Guilty has a good number of minor, deliberate, unsolved mysteries.
- Jim has stated that Harry will need to deal with every one of the Laws before the series is over.
- At the time of writing Proven Guilty, Jim was also working on the Dresden Files RPG
- The Dresden Files RPG has a lot of bonus material not in the books, including information on Baltimore, secret societies, and a primer on how time travel works (page 243). It even references PG specifically, proving if nothing else that Jim had these two books on his mind.
So with all that in mind, I think the simplest solution, as unintuitive as it may be, is: a Time Traveller (likely Harry), who is in a story akin to Prisoner of Azkaban: Harry goes back to a time we've read about before, and has his own plot, while guiding/avoiding/fixing the events of the previous timeline.
It would make a LOT of sense, and be a good story, because the events would be happening "now," so to speak. Instead of "Oh, so you're the one who fixed my model city 10 years ago? ...thanks, I guess?" it'd be "Crap, I need to fix this model city NOW so I can find the bad guy, and I need to do it and get out of here before Past Harry gets home!"
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I think that's what it comes down to, for me. Immediacy. Any theory that's just an unimportant minor revelation is just going to be incredibly unsatisfying to read, and considering that it's pretty clear how deliberate this was from Jim, I don't think unsatisfying is in the cards.