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.

• Note: that version of the theory is easiest with the interquel as canon, since the formation of the father-son relationship is the driving force of that film.

• While he was still with them around the day when Bambi met Faline, his father abandoned them or went missing at one point, which explains why he is never seen on screen, and why his mother keeps mentioning his sayings.
• He could've died. Remember when Man came to the meadow, and you heard a gun being shot? Maybe it was poor Thumpy's dad Man got.

• Which would explain why only four of Thumper's sisters are present in the midquel.

• Could be "Aunt Ena" is just a very good friend of Bambi's mother and the title was honorary.

• Flower was simply the second most effeminate male skunk in the forest, and happened to run into the first. Their kit is adopted.