To answer your question: No, if the protagonist disappears before the end of the story it wouldn't just irritate the reader, it would likely not make sense, or maybe not even work.
I'll go into why below.
Main Character and Protagonist
That your story seems to be carried by two characters might be because one of them is the main character and the other is the protagonist.
These terms are often used interchangeably to describe the "hero" of the story, but they mean slightly different things. Dramatica defines the difference as:
- A Main Character is the player through whom the audience experiences the story first hand.
- A Protagonist is the prime mover of the plot.
- A Hero is a combination of both Main Character and Protagonist.
I.e. the main character is usually the carrier of perspective. In a first-person singular story, they'd be the "I". The protagonist carries conflict and is the one fighting the antagonistic forces.
A famous example of this split would be the Sherlock Holmes stories where Dr. Watson is the main character and Holmes is the protagonist.
Maybe one of your characters is the main character and the other the protagonist?
Main Character, Protagonist, and the Climactic Moment
So, back to your question: do they all need to be present at the climax?
I think the most important part of the climax is the Climactic Moment. The Climactic Moment is the point in your story that, when it has ended, takes away all conflict and effectively ends the story. I.e. the Climactic Moment is the final showdown between the protagonistic and antagonistic forces. The Final Battle. (See the link above for examples where the genre is not "battle action"...)
After this scene, you can do some tying up of loose ends, and it's common to show "the new normal" but this could as well be done in an epilogue. Regardless, you don't spend much word count here. At most a few pages.
It is obvious if you're going to have a showdown between protagonistic and antagonistic forces, you need to have the generals of the respective forces present (I.e. the main antagonist and the main protagonist).
And if you've done your main character right, by this moment the reader is in sync with their feelings and thoughts, and removing this character from the most important event in your story would deprive the audience of the chance to experience it at top quality.
So I think all of the heroic functions, the main character as well as the protagonist, must be present in the climactic moment.
I'd even go so far as to say your main character/protagonist/hero should be present not only in the climactic moment but in the middle and the beginning as well. Even in the very first scene, preferably even the very first sentence.
So what to do if your story's protagonist or antagonist isn't present in the climactic moment?
The most obvious answer is to rewrite the story to make them present there.
But it could also be possible that the character you think is the main character/protagonist/hero isn't really. Otherwise, why would they wander off from the most important moment in their story?
Maybe some other character, present in most scenes of the story is the protagonist, and/or the main character?
Maybe the story can be rewritten to make that happen?
If you give the perspective and the role of Main Character to some character that is present in most of the book's scenes, and especially the beginning and the end, you could introduce a Dr. Watson that could make the story work without having to do so much about the conflict and the battle between the protagonistic and antagonistic forces.
Well, you may have to bump some protagonists up the ladder to make the protagonistic presence stronger in the final battle. And your current protagonist should then probably turn out to not be the strongest opponent to the antagonistic forces... I.e. you'd need to redefine who your main protagonist is and you probably need to plant that earlier in the story as well.
If this is a first-person singular perspective you'd have to cut all scenes where the character isn't present, or rewrite those scenes. But from your question, I surmise it's not, so then it's just about shifting the third-person perspective over to this character instead. (And one easy way to do that is to rewrite in first-person "I" and then either keep it or shift it back...)
It is also possible your story has more than one main character/protagonist, but in that case, it's preferable that their stories converge in some direct or indirect way in the climactic moment. E.g. one storyline causes the conflict and especially the climactic moment in the other storyline, or the different main characters/protagonists, having wandered in their own adventures most of the story comes together (by plan or serendipitously) to fight the antagonistic forces in the final battle.