Now, I’m just thinking aloud here, ain’t nothing to it really, but I’ve never liked the explanation that the Entity caused Marle’s disappearance and then timed her subsequent reappearance just so. As the Guru Gaspar put it—at least I think it was him—if you happen to be important to the space-time continuum, you get special…er…privileges in the legers of existence. Consequently—in-game timeflows notwithstanding—going by the plot-timeline by which this importance to the continuum would be judged, it is the case that when Marle disappears neither she nor Crono had done anything that would unequivocally merit them the status of “special.” Really, all they had done at that point was travel through time once each, which on its own I don’t think would be a sufficient condition to merit this specialness in either of them, as evidenced by NPCs such as the Gurus who were edited right along with the timeflows around them at the various milestones in history effected by Crono & Co.
I can’t imagine that the Chronoverse is so poorly designed that it could be undone by a paradox. Either it can handle paradoxes, or paradoxes can’t exist. When Marle was mistaken for her ancestor, the space-time continuum cancelled out this little contradiction by canceling her out, which would have to be the low point of anyone’s day, I’d imagine. Notably, however, the timeflow itself did not seem to be edited around her. This raises the important question: does every change to a timeline result in a timeline split, or is this limited to “special” events. If so, perhaps then the definition of an entity special to the space-time continuum would be that said entity perpetrates a “special event.” Marle’s self-eradication, not being a special event, would not have created a timeline branch; it merely nullified her from the (singular) timeline.
So far, everything is consistent. When Crono & Co. restored history closely enough that Marle would once again come to be born, she was reinstated—which raises important temporal implications as to the nature of matter-energy that is supposedly “erased” from existence by a timeflow edit.
Now, why did Marle not disappear the instant she arrived in the past? Obviously, because if she had done so, she would not have been able to erase herself from the timeline by being discovered! And if you’re not comfortable with that implicit way of looking at it, then by carrying the logic out forward directly, it would stand to reason that the event of Marle’s discovery and mistaking for Queen Leene did not coincide instantaneously with the event by which whomever would have found Leene was informed of Marle’s discovery/mistaking. Thus, to put it in the simplest practical terms, Marle didn’t disappear until the guy who would have found Leene was told that “Leene” had already been found. That gave Marle a few hours in 600 A.D. before her disappearance before Crono’s eyes, which, by reasons of dramatic coincidence and artistic license, happened to exactly coincide with Leene’s rescuer(s) being called off.
A more difficult question is why did Marle not reappear the instant Leene was rescued. My proposal is that the rescued Leene, having just been through a major ordeal that she had not undergone in the more original timeline, was in great personal flux. Traumatic events change us, yes? And with Leene in flux, her destiny was also uncertain, and thus there was no reason Marle should suddenly reappear. So, because we’re dealing with a game of destiny and time travel, I can hold it plausible that the Good Queen Leene did not “click” back into her original course of affairs all at once. This only happened after she returned to the castle and spent some time with the King—at which point, again by reasons of dramatic coincidence and artistic license, happened to exactly coincide with Crono running back up to where Marle had disappeared and seeing her then reappear before his relived and eager eyes.
This would explain Marle’s disappearance, the lack of a timeline branching event, Marle’s reappearance, and the apparent discrepancy between this event and subsequent events that would have had similar effects on party members had they not become “special” by then, and all without invoking the Entity or other supernatural forces…other than a good dose of wild speculation into the nature of temporal mechanics, and as for that, there ain’t nothing to it. =)
~ Josh