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Most of the evidence that lends to this having happened is in season 5 episode Yang 3 in 2D, so I've only compiled from it if you want to rewatch.

1. "Why can't I remember it?"

Shawn's perfect recall has been shown to fail him on exactly one other occasion. In the episode of Last Night Gus, when he and the others discover they had been drugged. But for some reason, in the year 1990, his memory randomly cuts out as he sees the back of Yang's head before she turns around in her driveway. He can't remember when he met her, can't remember speaking to her, not even his mother taking a photo of them. Either he was drugged around that time– which seems unlikely– or what took place was so traumatic, he buried them or dissociated away the experience.

I also think that when Late Night Gus occurs, he lets some of his darker feelings about what Yang did to him– that he's semi-aware of– slip out. In his rant about losing his gift, it seems there's a lot of genuine anger that it'd been "taken" from him.

2. "It was a sky blue shirt with a dark blue collar."

Something happened to the shirt he wore on that day. Neither of his parents ever saw it again. He's wearing it in the picture, so it must have been on when his mom took him home. I'd bet he was the one who threw it away, burned it, or shoved it in a nook and never wore it again. It's also just slightly possible that either Yang broke in and stole it as a momento, or Yin got his hands on it, knowing it held DNA evidence against her and could have gotten him caught. In any case, a pair of pants probably went with them, but with those, one looks like the next and wasn't noticed to be gone.

Henry's reaction is extremely telling, too. World's not so great dad that he is, knows something is very, very wrong. He throws himself into trying to prove... what? What's the disturbing possibility he's so desperately avoiding? I think it's obvious.

3. "Shawn, I'm insulted. This was our moment."

It's explicitly stated that Yang was attracted to Shawn as a child, Yin saying she "took notice of the pre-pubescent [Shawn] and developed an unhealthy crush." She also told his mother he was handsome and had kindness in his eyes.

What's open for interpretation is her saying the creepy line: "Shawn and I have a romantic history together. And I deserve to see his bedroom." Yes, it's revealed to be a hint she dropped as to the title of the class Allison was taking, but still...

Given her overall demeanor, the way she acted toward Yin, her father, a serial killer, it wouldn't be surprising if he abused her in a similar way.

4. "I was out looking for Shawn...

"...cause he was late for dinner." If attempting to narrow down the time in which this may have occurred. It's concerning that Shawn's mother had to hunt him down because he was late, and she didn't know where he was. It's completely possible there was a window that he was in the house with her, or the car in the driveway, before she got there and found them standing outside.

5. Fleeing the scene

Shawn's mom said that Yang disappeared within a week of meeting him. Yin probably got wind of what had happened, or she herself momentarily had the presence mind that what she'd done was wrong. And they got out of the neighborhood as soon as possible in case a report had been made.

6. The Subconscious Ich