The way I'm assuming that works is that the documents (physical or otherwise) all still exist, they just don't have his name, photo, or any of his details on them. They're either blank or magically redacted to the point of uselessness. So yes, hypothetically there's a bunch of blank files out there mysteriously filed between "Parker, Perry", and "Parker, Peyton", lots of weird blanks spaces in news articles, directories, yearbooks and the like. Probably the most confusing thing for MJ in particular would be the selfie of herself, taking up half the screen and she's
smiling. Which is downright weird unto itself.
So yeah, from all that an especially obsessive, thorough and paranoid person may be able to reconstruct enough to deduce that someone called "Peter Parker" was erased from existence in his late teens, but since The Question is a DC character, not a Marvel one, the odds of that are slim!
Assuming the rules of time travel are still the same, they're all technically variants of the ones we saw in the movies, taken out of their universe at the moment they learned Peter was Spider-Man. It's been ages since I saw the Rami films so I don't recall exactly when that happens (and I only ever watched SM3 once when it came out on video) but in Norman's case I think that would be right after the thanksgiving scene when he notices the cut on Peter's arm. Presumably he was taken just after when the reality fully sunk in (to account for how he came through with the suit and glider) and would likely have returned to that same point in time. What point is space however is an interesting question since they all seemed to arrive more or less in the same place they were in their universe; Otto was out by the Hudson, Max was inside the power grid, Eddie was in that hotel room in Mexico etc, so it stands to reason they all either reappeared at the same time they left, but in the place they were in the MCU (Liberty Island), or where they were originally.
So Harry at least would arrive in a world where his son is still very much alive. The logistics of Otto's arrival are a little tricky since in the original version of his timeline, he came to his senses long enough to destroy his machine, but die in the process mere minutes after he left. Maybe his grip on sanity would only ever be temporary since the chip was still fried, and he was taken *after* he fell into the river, so this version of Otto should have returned to an already destroyed machine, though still in a world where Norman is already dead, and Harry is on the path to following in his footsteps. Maybe he helps Peter save Harry, or at the very least stops Clint from falling into that supercollider.
