Despite getting engaged and having kids together, Emily and Alison are currently on the rocks. Unfortunately it seems trauma from Emily's past has caused a roadblock in their relationship. Ali vaguely hints at their relationship status during a conversation with Mona in the season premiere of The Perfectionists, saying that although they aren't physically together, she's not completely abandoning hope for a future with her one true love.
"Emily loves me. She just can't get past the past," she explains, hinting at their ongoing trust issues. "We're happy, and then we're not. It all comes back to trust. But I'm not giving up."
Despite not seeing Mitchell's character in the flesh in the premiere, we do get a glimpse of her as Emily unpacks her new place in Beacon Heights. In addition to boxes and cute home decor, she takes out an incredibly cute picture of her and Emily holding the twins and puts it on display on her mantel with a longing expression.
So for now, it seems Ali's focus is on leaving the girl she was in high school behind for good and making up for her past actions by helping the students attending BHU. And as for Emily? We probably won't be seeing her for a long time (if ever), but remember that this is the PLL universe — anything can happen.