Taichi and Gabumon end up separated together after Mugendramon's attack on Meicoomon, which caused distortions out of fear and loss of control. They're both screaming at the top of their lungs, calling out to the others to see if they can reunite and Gabumon drops the "-kun" when calling for Yamato.
I feel like Gabumon instantly felt a deep connection with Yamato, showing admiration from the start.
Taichi seems to find it funny but doesn't say anything at first. However, he can't help himself and starts teasing him about it later when they find Plotmon and Hikari. While explaining what happened, Gabumon refers to Taichi just by his name, telling them that after Mugendramon's attack, a distortion appeared right in front of him and when he woke up, he was right next to "Taichi". Just like that, no honorifics.
It's such a hilarious dynamic because even without his memories, Gabumon's subconscious puts Yamato on this respectful pedestal, while treating Taichi like a total peer he can banter with.
Meanwhile, Yamato ended up with Agumon, Koushiro and Gomamon, and it's so great when Koushiro shows Gomamon and Agumon pictures of all the chosen children, including their respective partners, Joe and Taichi.
And right when they're talking about Taichi, it's like Yamato remembers their duty and seemed annoyed by how scattered they are and starts walking to look for the rest, and Koushiro and the digimon hurry to follow behind.
Based on Agumon's words, it seems both Koushiro and Yamato had been telling Gomamon about Joe, but Yamato hadn't said a single word about Taichi. This makes Agumon wonder if Taichi and Yamato don't get along, but Koushiro immediately says that they actually get along well, and Yamato snaps back with a quick "no, we don't". Agumon then asks if he doesn't like Taichi, to which Yamato replies "I don't hate him. I just expect too much of him", while placing his hand on Agumon's head as Agumon looks up at Yamato's worried face.
The moment is interrupted by a train that almost hits them, but Yamato shields Agumon with his body and Koushiro does the same for Gomamon, and they jump off the tracks.
Once they catch their breath, Agumon asks what they were talking about and Gomamon reminds him it was about Taichi and Yamato, making Yamato say to drop it. Agumon then changes the subject by saying that when he sees Taichi, he's going to ask him for takoyaki, which cracks Koushiro up and breaks all the "tension".
As night falls, they all see through a distortion that Sora is in danger. The first ones to jump to her rescue are Taichi and Gabumon on one side, and Yamato and Agumon on the other. Flashes of Gabumon's Fox Fire and Baby Flame from Agumon, shield Sora and Piyomon from Mugendramon's attack, and the partners finally reunite. Gabumon gets back to Yamato, and Agumon reunites with Taichi.
Yamato praises Gabumon for his timely feat, while Agumon joyfully rushes toward Taichi, biting his arm like an anxious puppy who's now happy after being separated from his family.
Later on, when Yamato, Gabumon, Taichi and Agumon (with Hikari and Plotmon running behind) act as bait to let the others escape the ship where they're cornered by MetalSeadramon and Dark Gennai, there's this hilarious moment. Yamato helps Gabumon launch an attack by throwing him into the air, so Gabumon gets so proud of himself for taking on such a massive enemy that he hugs Yamato and blurts out "YAMATO!... uh... kun", and Yamato goes "Kun?" in surprise.
Taichi exposes Gabumon, telling Yamato that he had been wondering what to call him. Gabumon yells "TAICHI!" in embarrassment, only for Taichi to fire back with "WHERE'S MY "KUN"!?" lol. It kills me that Taichi demands the honorific from Gabumon just because he used it with Yamato. What a way to tease him.
Taichi and Yamato risk their lives to protect Agumon and Gabumon from MetalSeadramon, and Agumon and Gabumon dive into the sea to rescue them, confused about why they'd put themselves in danger like that. When Taichi and Yamato just say they don't want to lose them, Agumon and Gabumon tell them they want to be stronger. That bond triggers their Mega evolutions into WarGreymon and MetalGarurumon, and they team up to defeat MetalSeadramon.
Digimon Adventure tri: Loss | Taichi, Gabumon, Yamato and Agumon.
Having the distortions split Taichi and Yamato with each other's partners is what I think makes sense of Omegamon's reappearance later in Coexistence despite the reboot, since it let the digimon bond with the other half of their fusion duo.