Capcom's inconsistent about this part of the lore, in RE6 Sherry says Claire and Leon saved her implying the more correct version is Darkside Chronicles, and in the remake they scrap majority of Leon and Claire's interactions from the original making it false that they bonded
The thought Claire being in RE9 always felt wrong to me, and I couldn't put my finger on why.
I finally realized that it's because RE9 subtly tells us that Leon doesn't know what happened in Claire's RE2 campaign. Those stories have never been exchanged between the characters.
The fact that Leon has to ask Sherry if there's even an orphanage nearby the RPD means that neither Claire nor Sherry ever told him what happened to them that night in the city.
And if Leon doesn't know about Claire's campaign, then Claire probably doesn't know about Leon's campaign -- which means that the only other regular member of the RE cast who even knows that Ada exists is Chris. (Not counting Wesker, of course, seeing as he's... you know. Dead.)
This also explains Sherry's sort of blasรฉ "Been a while since you've been back there" remark to Leon when he says he's in RPD. She has no idea what the RPD actually means to him. The only thing she knows is that, when she met him, he was in an RPD uniform.
So, if Claire was in RE9, it would just be the three of them recapping RE2's events back and forth the whole game. And that might be cool for new players, but god that would be a slog to sit through for veterans.
Sure, you could make the argument that Capcom should've just wrote it so that the three of them have actually exchanged those stories, but the fact is that they didn't write it that way. And they probably wrote it that way for a reason.
And one of the biggest takeaways from this is that the thing that binds Leon and Sherry together is what came *after* Raccoon City. The sacrifice Leon made for her, and the lives they've lived since then.
For Sherry, the hero who saved her from Raccoon City will always be Claire. And that's beautiful in its own right. I wouldn't want it any other way.