I think he was missing for quite a few years
Yeah but we see them grow up and are in high school/middle school
That's just an AU. Not related with the main story if I remember correctly.
As far as I remember he was living in an orphanage with Flynn while missing and they did go to school together. He just has no memory of it because of Ethan.
Although considering how similar his current self and his teenage self look I don't know how Flynn didnt recognise him as an adult.
I am around chapter 60. Maybe I just forgot, but didn't the missing poster say Andrea was like 10-11 when he went missing? How come we see them in highschool together?