They're in a weird place! Selenia was someone that Flynn attached very strongly to when he first arrived in Aather because person who speaks with authority! It's very easy for Flynn to fall into his role as a knight with people who are commanding like Van. But then Selenia kissed him and things sort of became a bit more awkward on Flynn's side. Mostly it was an issue of too much too fast, because at that time Flynn still wasn't thinking of Aather as a different system from the Imperial Knights so for one, it was something that felt wrong to him as a knight-to-hero relationship, and for two, it wasn't something he'd even considered in terms of his own desires because he was still focusing super heavily on his duties as a knight-knight.

So Flynn sort of backed off out of consideration for his feelings and things were a little awkward for a while thereafter. They were on that sort of unstable footing until Selenia wound up giving away his love for a quest which freaked Flynn the fuck out. They somewhat resolved after that but then after the game where all of Sapphire died they had a disagreement on what's the right course for Aather, basically that Flynn supports the goal of Beauty and the realm regardless of what might happen in games and Selenia doesn't.

From Flynn's end things are still kind of...iffy. He's definitely not as close to Selenia as he once was because of the disagreements that they've had over Aather, justice, and the like, but Selenia does remain someone that he respects so he's just in general in a place where he's trying to figure out how to navigate their relationship.

What would Yuri do if someone stuck gum in his hair.