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It's symbolic of the fact that she's no longer screwed up, angry, and hurting herself. It's no coincidence that, in these scenes, her lip piercing has been removed and all of her tattoos are covered up. The end of Skye's story arc sees her inside a mental health facility, very much on the road to recovery, in a better mood and committed to healing.
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She promptly goes home and hurts herself to such a degree that she winds up in hospital. "It doesn’t have to do with the way that I look? Or that I have tattoos and piercings and cuts all over?” After Clay reassures her that he doesn't "care about that stuff," she gets out of bed, visibly upset and says, "You don't care." Here, her body modifications and cutting are one and the same - a cry for help. Skye herself puts them in the same category, during an exchange with Clay that occurs after he is too emotionally distracted to perform sexually. When it comes to Skye, 13 Reasons Why repeatedly draws a misleading and damaging parallel between body art and self-harm. It's a preamble to Skye's next appearance, in which Clay discovers she is still self-harming (a subject that was only briefly touched on in Season 1). Her first appearance in the new season is literally at a tattoo shop, where her ability to handle pain is contrasted starkly with Clay, who passes out halfway through getting a semicolon tattooed on his wrist. She's not the only tattooed person in 13 Reasons Why, but she is the only one almost entirely defined by them. When it comes to the teenage personalities in the show, Skye represents the laziest caricature. In addition to the sexual assault themes started in the first season, we now have heroin addiction, school shootings, a Brock Turner-esque court case, and self harm, courtesy of Clay's heavily tattooed love interest, Skye. Season 2 knows this, and, as a result, is far more heavy-handed about, well, everything. What made the show even more vital was that it was a major, unexpected conversation-starter among young people and parents alike. It was an unflinching look at the oft-dismissed hardships of being a teenager it was an examination of the lack of assistance for young rape survivors and it understood that, even when kids come from loving, supportive homes, they don't necessarily know where to go when they're in trouble. There are many things that Season 1 of Netflix drama 13 Reasons Why did phenomenally well.