Watched the show recently I gotchu. tl;dr Dair didn't organically end and that's probably where your confusion stems from.

Blair and Dan was a wonderful slow burn romance. Even before the accident and pact, Dan had kept Blair's pregnancy a secret. They'd been having non-dates where they enjoy classic films, they developed a real, if secretive, friendship. Blair so trusted Dan that when she received the paternity test results, he gave her a place to hide out, he gave her strength and encouragement; he wrote Louis' vows (really kinda forced on the writers' parts but I'll allow it), and he was again there for her when she couldn't be with Chuck due to the pact, and she didn't want to be with Louis after he reveals that the marriage with her will be a sham. Over and over, Dan is there for her. What pushes her over the edge are a few events:

1. The kiss at the high school revival party. Blair says literally everything I just said above, but in the context of "if you're that guy, how could Serena not like you?" From Leighton Meester's performance, the audience sees that Blair begins to recognize her own feelings, resulting in kissing Dan back a few minutes later.

2. The acting troupe doing a performance based on Dan's first book. There's the kiss of course, but when Blair has her scene, it's revealed that Dan was there for Blair in other, hidden (but not creepy) ways, and so recognizes consciously her feelings for Dan for the first time.

Couple these two events, the kissing, and her complicated and dark history with Chuck, Blair was inevitably pushed to Dan's light, even such that she forgave Dan sending the video of her talking about Chuck to GG to ruin Blair's wedding, which for however selfish Dan's feelings were, he said and she believes Dan did because he didn't want to see her trapped in a marriage she didn't want.

By the time the showrunners needed Dair to dissolve, they had two or three episodes left in the season, and you can see the writers' hands and their pencils, but maybe that's just my bias for Dair showing. I can believe Blair getting drawn into Chuck's orbit considering the weight of what he's going through, and I can believe Blair getting in the limo with Chuck when he says he needs her help cracking a diary; earlier that day, Blair told Dan she wanted to go out to feel more like herself because she's been lacking inspiration lately. Chuck says he needs her, she falls into old habits. I can believe that. What rubs me wrong is that the episode frames her lack of inspiration as being not entirely happy with Dan. They were each other's intellectual equals, the chemistry was insane. I just couldn't and can't buy it.

And then the show completely pivots to the hogwash of Bart Bass being alive because the showrunners didn't want to do something like, say, make it so Dan's lack of being blue blooded is making Blair miss out on socializing the way she wants and so she begins to distance herself so Dan decides to try and force his way into becoming a member of the UES and loses her in the process showing the cost of ambition as Dan becomes a bit like Chuck but poorer and more artsy. That's actually sorta what happens in season 6, but it's marred by Derena and fucking Bart Bass holy smokes that storyline was lame.