It's not in “
Bokutachi wa Benkyou ga Dekinai” because I can't even remember Takemoto Uruka on a bicycle, and she definitely does not make her first appearance in the story on a bicycle, and she's not reunited with Yuiga Nariyuki at that point (they're in the same school, he is enough of a buddy to let her copy his homework regularly, she's just friendzoned herself long ago).
If we are looking in the stories with a similar vibe — where (like here) the main character has been driven away by the
tsundere and then he discovers several other potential love interests, then it's not in “
Jimoto no Ijimekko-tachi ni Shikaeshi Shiyou to Shitara, Betsu no Tatakai ga Hajimatta” (I've just re-read the first fifty chapters and there's no such tomboy) and it's also not in “
Yumemiru Danshi wa Genjitsushugisha” (I've quickly navigated through a few series in the middle of the anime and there was no such scene).
The problem here is that the character of Hinata Haru makes a strong impression and it does not help (it rather tends to replace) my earlier memories of a different character with some (but not all) similar traits. And her other aspects (not limited to a sudden appearance of a tomboy on a bicycle) are also the things I have already seen earlier:
① an
osananajimi (a boyish girl) is mistaken for a boy to the point of asking her to bathe together? — Sawatari Ginbe Haruomi in “
Onii-chan dakedo Ai Sae Areba Kankeinai yo ne”
② a slender athletic girl changes her clothes in a locker room and the main character can see that? — many such cases, and the previous one was probably Yakishio Lemon-chan in “
Make Heroine ga Oosugiru!”
Unfortunately, multiple (branching) endings are a feature almost unique to “
Bokutachi wa Benkyou ga Dekinai” (the only other manga with such endings is “
Houkago no Goumon Shoujo”, I believe).