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Bambi's Mother faked her death.She realized that having Bambi become overdependant on her would be detrimental to him growing up to become the next Prince of the forest, so she abandoned Bambi at just the right time, knowing that the Great Prince would find him and care for him. In fact, her abandoning of Bambi may have been a Batman Gambit to get the Great Prince to break out of being The Stoic and care for someone, like he did when she and him cared for each other in the past before they drifted apart.
The midquel is set in a timeline similar to, but ultimately distinct from the original film.This would explain the more humanized personalities of the characters and general nature of the forest being somewhat different from that of the original film, but the events before and after the midquel still play out similar or identical to how they did in the original film, so that the two films could technically still work in tandem as a continuity and not have to worry about sweating the differences between them too much. Alternatively...
The midquel is only Semi-Canon to the original film.The general events of the midquel technically happened in some form, but how it literally played out would end up being different from how It was depicted in the film, and certain elements of the midquel would be considered either apocryphal or flat out non-canon to the overall timeline.
Bambi has a mild form of Post Traumatic Stress Disorder, and / or has Survivors Guilt and Chronic Hero Syndrome.
Bambi or the other animals don't wish any ill on man.Bambi is far too compassionate and graceful to wish vengeance on anyone, and the forest sees man as an impersonal force of nature to put up with, and something to be feared and respected as just another part of their lives.
Thumper's Father abandoned his family/went missing.
Thumper's Sister died/went missing during the winter.
Bambi and Faline aren't cousins after all.
Flower's mate is male.