You can't have your cake and eat it too.
I don't think your opening is in media res if it's cut with exposition flashbacks and the conflict hasn't started yet. To me that sounds like the opposite of in media res.
Diverting away from the main conflict for any reason breaks in media res.
Making assumptions by reading between the lines, I perceive the important information in your chapter is that something transpired between MC#1 and MC#2 that contributes to why MC#1 fails to prevent Antagonist from sowing chaos. MC#2 is only present in the flashbacks, but not in the main conflict scene.
My idea of in media res would be:
Opening scene: Conflict is underway. MC#1 attempts to stop/prevent Antagonist from doing the thing. MC#1 fails, and blames it on the earlier situation with MC#2 whom the reader has not yet seen.
Later in the novella: we learn that the situation between MC#1 and MC#2 was not quite as MC#1 believed, and also (separately) that MC#1 and Antagonist had some crucial interaction earlier too. The flashbacks work as minor plot twists or realizations of MC#1, who has good reason to re-examine these earlier interactions to make sense of his defeat.
Hindsight is 20-20, but right now, in media res, MC#1 does not have time to recall details of earlier conversations. He is acting now on adrenaline and instinct (and training, if he has it). Stakes are already high and escalating. MC#1, like the reader, is struggling to keep up with events generating meta-empathy for the protagonist as their "eye character". MC#1 is suddenly, unexpectedly in over their head, and so is the reader. Little wonder he can't prevent the Antagonist from doing the thing.
Why start mid-conflict, rather than show events leading up to it
In media res is the set up, not the climax, of Chapter 1. It starts high, and all falls apart quickly for the protagonist because he's misjudged the situation from the start. We get to see what kind of character MC#1 is: valiant, but maybe naive or over-confident. MC#1 has a blindspot which Antagonist has exploited, but the reader (and MC) don't recognize it. This is a character flaw that will need correcting before the protagonist can understand why they lost, or it's a handicap the MC can't avoid. MC#1 does not see this flaw, and neither does the reader, yet. These flashbacks are not important right now, they don't change the outcome, they just muddy the conflict and our perception of the archetypes. Worst of all, these scenes delay getting to the action.
The reader perceives that the hero has done everything right. The situation goes badly not because of mistakes, but because the Antagonist is very dangerous, potentially undefeatable. Our "hero" is suddenly the orphan/outsider at the top of the story, and starts with no guarantees.
Because of this, the reader also perceives the Antagonist as extremely dangerous. There is no ambiguity to their evil, no option to stop them preemptively in the flashback scene. The chaos has already happened. The threat is real. Chapter 1 is not about choices or options, MC#1 reacts out of instinct (and training) but can only make small corrective measures: minimize the bad, save who they can, accept that this can't be changed because the game is already lost. In media res is not about the protagonist's choices because they really have no options – it's about their realization of failure. It's the sudden downward slide where they are stripped of their status quo.
Quite frankly, we don't need a lot of worldbuilding or set-up to understand that the hero is losing and that the villain is bad. The hero might have ambiguous feelings about the redeemability of the Antagonist, but the reader needs to see him as 100% evil to be convinced the stakes are real and not just a heartfelt misunderstanding between friends. There are no stakes from a "maybe" Antagonist, the reader should not have doubts the antagonist is willing to go all the way, even when the protagonist feels unsure. We don't need to know about the earlier scene between the two yet, again that muddies the situation: clear goodguy who believes the situation is redeemable and fixable; clear bad guy who has already decided the world needs to end. Of course there will be more to it, but that's not important right now.
To defend their ego, and psychologically unprepared for a surprise defeat, MC#1 reaches for an explanation and blames (or recalls) the earlier situation with MC#2. "If that had gone differently, this would not be happening!" The reader who is hooked by the direct action of the conflict and solidly identifies with the protagonist, hears an unsubstantiated explanation about a third party and an earlier incident. Now we need to know about the earlier situation and this other character. That scene becomes much more important after-the-fact than as a set-up (assuming there was a plot-reason for that scene).
When the reader actually meets MC#2, we see a character that does not entirely conform to expectations, which is great because we are already a bit suspicious and have been seeded doubt. This might be the first hint that MC#1 is unreliable, or the first evidence of their flaw; but also maybe MC#2 is the unreliable one: a frenemy or a de-stabilizer. The reader's flexibility to re-interpret that flashback incident is lost if there is no mystery to the situation. In the as-written version, we've already seen the incident presented as "factual" by the narrator. That earlier scene probably gave us some exposition, presumably to set up the stakes or establish a relationship – but if MC#2 isn't a direct actor in the in media res conflict, she probably shouldn't be seen yet. This flashback doesn't carry any weight with the reader being presented so early in the story before the conflict even begins. It's just a detour. After the in media res defeat where the hero makes reference to earlier events, the flashback has gravity and importance that it didn't have before. It's not infodump and set-up, it's explanation and resolution – or even better, it leads to another interpretation of events for the reader, otherwise known as a plot twist.
Why have 2 flashbacks in the opening scene at all?
The objective "truth" of the flashback scenes should be withheld, until it's clear the events are the subject of interpretation. Present those scenes initially as the MC remembers it (probably not through flashback but just through the MC's testimony), then present it again as the other MC remembers; same for the second flashback with the Antagonist, so there is some dispute about what really happened. By visiting these scenes late in the story, you have opportunity to explore character perspective and reveal relationship issues the MC was blind to at the beginning.
Obviously, I am not in any position to re-write your novella, so these suggestions won't apply to your story without a major re-think. But the goal of in media res is to skip all the lead-up exposition and start in the middle of the unfolding action. I honestly can't see why a story begins, and then hops around to 2 non-linear events earlier that same day, before getting to the action. I assume you have your reasons, but it seems like 2 or 3 false starts before you get to the in media res conflict. For me that doesn't fit the function of either in media res or flashbacks. My suggestion is just write the main scene so we can see the archetypes be who they are as their status quo. Keep the reader in the present where the stakes are escalating. After everything goes to pot for the MC, the reader will share the goal in reviewing the objective truth to these flashback moments.