I've had a thought on the "Who Fixed Little Chicago?" question, and my current front runner is...
...
...Bob
Of everybody/thing that we've seen by that point, Bob fill the Means/Motive/Opportunity requirements the best.
Means:
We have from Bob that building Little Chicago is something very few individuals could do. Whoever fixed it needed to have a lot of magical/thaumaturgical knowledge as well as an intimate, working knowledge of LC to know that there was a flaw, let alone fix it. That eliminates most of the Mortal world, and Nevernever.
Bob, however, helped Harry build it and was there every step of the way. He probably even had a direct "hand" in some of the really fine, fiddly bits.
Opportunity:
Anything that would want to fix LC would have to be able to cross Harry's threshold AND circumvent his wards... and a very stubborn steel door. We also know that Harry doesn't have any mirrors in his apartment, denying easy access to those who can/do use them. They'd also have to know about Harry's lab (all things considered, not a HUGE hurdle, but the trap door IS cleverly hidden by a throw rug).
None of that matters for Bob, as he is already inside, in the lab (where, by the by, he would have seen anyone who came in).
Also, Bob knows about LC. At this point in the story, very few people know about it... Basically limited to Harry, Bob, and maybe Thomas & Mouse. If you don't even know about it, how can you know that it has a fatal (literally) flaw that needs to be fixed, or how to fix it?
The "Means" part eliminates Mouse (no thumbs) and Thomas (doesn't know enough). Harry didn't fix it because he didn't know it was broken.
That leaves Bob.
Motive:
This one is sticky. I can't come up with a clear motive for Bob, other than he likes Harry, and doesn't want Harry or himself to get blowed up.
Now, here's the sticky part.
Mab
She's the queen of Air and Darkness. Bob is an Air spirit. I'm WAGing that perhaps Mab was able to speak to Bob, whose nature and history puts him in her domain, and told him that LC would or could go BOOM! if Harry tried to use it, and had (commanded) him to fix it.
While I'm WAGing I'll throw out two more:
1) Mab did this while tending to Lea's "garden" during Lea's "Reeducation", and fulfilling Lea's duty of watching out for Harry.
2) All beings on the order of power that Mab is don't see time in the same manner as mortals. I'm guessing that she has a similar perspective as Uriel (ie: time isn't linear, like driving in a car, but laid out to see in its entirety, like a street map). She either saw that it would explode, or looked in and saw that they missed something.
Now, as to why Bob doesn't seem to remember this. I think that it was actually another aspect of Bob's personality that we haven't seen onscreen yet, that Bob may not know about himself (like Evil Bob), and Mab was talking to THAT Bob.
We know Bob has a significant history in Winter, and specifically with Mab. We also know that parts of him are hidden, even from himself (like Evil Bob). I think it could be possible that there's a "Winter Bob" from his time in Winter.
One more possible cluebat: When talking about it afterwards, Bob repeatedly refers to whoever fixed it as "He". Bob could have said "They" to account for the fact that it could have been female (or identified itself as such), or could have been plural.
The repeated "he" could have been Bob's subconscious (or however that works for spirits) way of telling Harry that he did it.
Thoughts?