I seem to recall that it was a glitch, part of the game rerunning past data, specifically, the scene where you first encounter Aeris. When she's near the flowers and Cloud is exploring the church, and can talk to Reno. Walking back towards the flowers, which would trigger the confrontation/escape (the "don't walk on the flowers" scene), initiates a check which makes the game realize you're past that point, and removes Aeris, who should never have been there.

But, that's just what I remember hearing about it. It could have just been a theory or explanation.