Flynn Scifo was not born yesterday, nor was he stupid. He did not get picked to be Commandant simply because he was the only pick, even if it seems like that sometimes. Flynn had other qualities to him that makes him an excellent Commandant, even things that Alexei in his glory days lacked.
One such thing was his ability to pick up on clues and subtly gather information around him about things people try so hard to keep a secret from him.
This seems like an obvious trait for a Commandant to have, yet Alexei had been blind to his own weaknesses, and worse yet, lost sight of the very thing that was instrumental to his downfall: the Dein Nomos. Flynn, however, would not make the same mistake. So he keeps a watchful eye on things, his ear to the ground and he hides it all behind his usual smile and righteous attitude people have come to expect of him.
People come to think they know Flynn. They lump him into a stereotype, and while he did fit it most of the time, he also uses it as a shield so that others might not pick up on the traits many might say were 'anti-Knight.' He has Yuri to thank for such traits.
Flynn was not stupid. It took him some time, but he did find out it was Sodia who shoved Yuri off Zaude.
He also found out why.
He has yet to say a thing to her, even after months of the world being saved from the Adephagos.
Perhaps it was cruel, but so were her own actions. Flynn believes her own torment and self-placed agony was punishment enough for her deed and foolish thinking. So he puts on a smile when she seems so uncomfortable and awkward, and he lets her think he has no idea. Sodia has such a guilty face it was a wonder anyone thought he wouldn't pick up on it.
He turns a metaphorical blind eye to her guilt though. He'll let it eat at her. Not just for vengeance, no. She has to be punished severely, and it should be in a lawful way, but Flynn knew that was not powerful enough for such a transgression. So he lets her beat herself up over it.
He also wants her to get a spine and actually confess to it herself to him. She might never. He might feel sorry enough to finally tell her he knows. For now though, he pretends he doesn't, but he keeps an eye on her to make sure she keeps herself in that state of self-agony and won't repeat her mistakes again.
A shame Yuri wasn't so easily pushed into the metaphorical corner.
There was not much Flynn could get Yuri to feel guilty on, not when he felt so strongly in the right for his actions. It was frustrating, but Flynn was patient. Another trait Alexei ultimately lacked; if he were a bit more patient, he probably would have completely succeeded and lived to tell the tale.
Or he'd realize what he did and stopped himself, but while Flynn likes to think there is good in people, he sort of knows better than to bank too much on that now.
Yuri was a good person. Flynn knows this because he just knows Yuri, but Yuri had so much go wrong and seen so much go wrong, Flynn was not that surprised when he snapped.
Flynn is just happy he snapped on people who deserved their fates, even if it were the wrong thing to do. After some thinking, Flynn turned a blind eye to the past actions.
He also knew a part of Yuri was a bit regretful to have stepped over that line. He can see it sometimes. Yuri hides it so well, but Flynn knows what to look for.
And he lets Yuri suffer it. He speaks nothing of the deeds and he lets Yuri work it out, even if it hurts him to some extent. Maybe one day he'll sit down with Flynn and talk it over.
Maybe he never will. But so long as something hurts, Flynn was content.
It wasn't like he wants his best friend to hurt. He just wants him to learn the lesson, to realize even if it were to men who deserve fates worse than what he doled out, it hurts. To kill monsters was one thing, but another human… it should hurt.
Flynn is relived it hurts. It meant Yuri was still good inside.
If it didn't hurt, he would be terrified, to be honest. Terrified and ready to take arms against Yuri and bring him to lawful punishment, even if it meant death to him.
There was a lot Flynn turned a blind eye to, not just about Sodia and Yuri, but everyone in the Brave Vesperia group. From petty things like Karol's break in into Aspio to Rita's assault on various knights to Judith's destruction and vandalism of blastia to the deception of the empire that was on Raven's record. "Little things" as Yuri would say that people didn't think Flynn would figure out and link to them.
The "little things" matter. They burrow in and become bigger things and gnaw from the inside. They link together bigger issues that bring on the guilt.
And Flynn lets the little things eat at them. He just knows they're there, and lets them sit in it. Sometimes, that was worse than lawful punishment.
Of course, it was also the only way to punish them, given they had been pardoned of all their previous crimes. Not that Flynn would disagree to that pardon, or has his own demons in the closet ready to rip him apart.
He's just glad they would feel guilty. Hopefully, it meant they learn, and he can continue to hear, write and report only good things about them.
But just in case, he watches, listens, and turns a metaphorical blind eye so they don't know he's watching.