More than I can count! Let me try to remember as much of them as possible and list them.

Sadoswap AU: While their D/s dynamic is the same as canon, Cy's a masochist and Lynn's a sadist. They make it work.

Teacher AU: Cy is 17 years older than Lynn and also her high school Math teacher. Grooming ensues.

College AU: Lynn is 17 years older than Cy and also his college History professor. Horny disaster ensues.

Baby AU: Cy somehow gets Lynn pregnant and makes her keep the baby, a little girl they name Olivia. Cy's a surprisingly good dad while Lynn struggles with paranoia due to fearing for her daughter's safety at the hands of her own father.

Divorce AU: Cy doesn't make enough concessions for Lynn so she ends up divorcing him. They manage to remain friends but Cy will never get over Lynn. She eventually finding a new Dom in Alec, a terrible, terrible man but great fuck, while Cy goes through a bunch of girlfriends who all suspiciously look a lot like Lynn.

Yaoi AU: "Lynn" is a bi guy named Eden who's been in a civil union with his best friend Cy for years and isn't allowed to tell anyone because Cy would rather die than publicly admit he's dating a man. It takes even longer for Cy to realize he's in love.

Kate Wife AU: Cy doesn't meet Lynn in college, doesn't develop any kinks, and instead goes on to marry Kate Anderson, one of his former students. Much more removed and less social, he meets and befriends Lynn after transferring to a new school.

Poly AU: Cy never fucks up his relationship with Kate and gets to keep her in her life, resulting later in a polycule with Lynn, Kate and Isabelle, with him at the center. They're all very happy.

Traumaswap AU: Cy is the one who goes through Lynn's "canon event" at age 19 while she remains blissfully untraumatized. It dramatically impacts both of their personalities and their relationship. Stone traumatized top VS silly fucked up puppy.

Hannibal AU: A CyLynn take on the show "Hannibal", where Cy plays Will Graham, Lynn plays Hannibal Lecter, and Isabelle plays Abigail Hobbes. Cy struggles with the half-unfounded bad reputation he has due to his dating his students at the FBI academy while Dr. Wu, his therapist and friend, seems to be pushing him towards indulging increasingly darker instincts....

Twins AU: Lynn and Eden are twins who are both into Cy and competing for his attention. Improper things happen in every direction of that triangle.

Furry AU: Everyone is an anthropomorphized animal. Lynn's a borzoi, Cy's a panda, Kate is a raccoon and Isabelle is a Silken Windhound. It's all very fluffy. Lynnzoi wears the cone of shame a few times.

BONUS ROUND: AUs that were created by fans!

Therapist!Lynn AU: Lynn's Cy's therapist. She secretly gets off to the crimes he confesses to during his sessions with her.

Roleswap AU: Cy's a traumatized rape survivor PhD student trying to rebuild his confidence by pursuing a mostly asexual BDSM relationship with his Physics professor Evelynn Wu, who tries to contain her callous sadism for him.

Yeah, casual drinking, not that impulsive though. Meanwhile Cy's the one who has to deal with addiction (cigarettes)

Traumaswap Lynn is unabashedly a freak, and a bit careless too sometimes, so she does often push Cy's limits.

Significantly less than canon Lynn, but Cy still watches her alcohol consumption.

Because Cy doesn't get as into torturing Lynn on an emotional level and he doesn't cheat on her out of malice but more out of need to take breaks from kinky sex, it removes any motivation he'd have to go that hard on her.

No, there's quite a few components in the Rube Goldberg machine leading to that in canon missing in this AU.

He's not as squeamish around sharp things as canon Lynn is, but he definitely can get triggered, so him being able to do kink stuff with that really is a matter of when and how (when he's older, and probably mostly with Isabelle). I could see him play the maso side with Isabelle on occasions, less with Lynn because she's a bit too unhinged to be trusted with that kind of power.

He's a bit less secretive about it there than she is in canon, but she still never gets the full story.