At the end of Avatar: The Way of Water, Kiri can use her special powers underwater without having another seizure, but it is never explained why. Earlier in the film, Kiri is diagnosed with epilepsy after having a seizure underwater while at the Soul Tree, and Jake tells her not to bond with it again. However, that does not mean she is barred from bonding with all living things.
Kiri, Jake and Neytiri's adopted 14-year-old kid, being formally diagnosed with epilepsy in Avatar: The Way of Water is wonderful representation for those living with epilepsy in real life, as epilepsy is rarely depicted accurately on the big screen. Using seizures and epilepsy as a plot point, without it ostracizing Kiri, adds another layer of depth that connects the film to the real world. Jake is distraught when the doctor tells him that Kiri should not connect to the Soul Tree any longer, as any father would be, but the rest of the film makes it apparent that Kiri's epilepsy doesn't prevent her from bonding with other creatures.
Kiri's Powers Let Her Bond Without Having A Seizure (Outside The Soul Tree)
It appears the only time Kiri cannot perform tsaheylu (Avatar: The Way of Water's Na'vi terminology for bonding with a living creature) is when she connects herself to the soul tree. She can connect to the Skimwings to ride them at the film's climax. When she performs tsaheylu underwater to flee Quaritch with her siblings, she can move flora and fauna in the water telekinetically, including light-emitting fish that help Neytiri and Tuk escape the SeaDragon.
The Soul Tree is fundamentally different from Kiri's other moments of tsaheylu. Epilepsy in humans can present itself in various ways, with seizure triggers varying from person to person. It's possible that something in the Soul Tree is a seizure trigger for Kiri, which is not present in other organisms she has attempted to connect with. Regardless, Kiri's epilepsy and connection to Eywa are some of the biggest questions Avatar 3 will need to answer.
Kiri's Soul Tree Seizure Could Have A Deeper Meaning
Kiri having a seizure specifically at the Soul Tree could have a deeper meaning. The Soul Tree is the heart of Eywa, the goddess that guides all of Pandora. Avatar: The Way of Water illustrates that Kiri has a special connection to Eywa, which means she can wield powers and feel her more deeply than other Na'vi.
The seizure occurs when Kiri asks Grace, via the Soul Tree's connection, who her birth father is, a mystery that remains unresolved. However, before Grace can respond, Kiri begins to seize and is pulled away from the Soul Tree. Eywa may know she isn't ready to hear who her other birth parent is and induced the seizure to stop Kiri's search. Some even theorize that Eywa herself is Kiri's "father" in Avatar: The Way of Water, with Grace becoming pregnant in a magical, spiritual way. Whatever the reason for Kiri's seizure in Avatar: The Way of Water, hopefully, it will be explored in future Avatars to provide more answers on Kiri's purpose.