I am almost certain that what im about to explain is simply not possible using parented bones, im asking just to be fully sure.
Assume that i have a leg animated in my custom format, it consists of 3 transformations(The upper part of the leg is rotated, the knee is rotated and the foot is rotated) the rotations each have different values (eg the leg was rotated 30 degrees in the x axis for example, the knee was rotated 60 degrees in the z axis and so on)
I have exported the bones to blender and built a hierarchy so leg has a child knee which has a child foot (Leg -> Knee -> Foot)
Now i want to convert the animation as well but i believe this is not possible as in blender rotating the leg would affect knee and foot aswell which would make the animation look wrong so i believe my only option is to export them as single bones(unless theres a way to keep them parented but i highly doubt it)