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Upgrading to Unity 4.0
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Upgrading to Unity 3.5

If you have an FBX file with a root nodeA transform in an animation hierarchy that allows Unity to establish consistency between Animation clips for a generic model. It also enables Unity to properly blend between Animations that have not been authored “in place” (that is, where the whole Model moves its world position while animating). More info
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marked up as a skeleton, it will be imported with an additional root node in 3.5, compared to 3.4

Unity 3.5 does this because when importing animated characters, the most common setup is to have one root node with all bones below and a skeleton next to it in the hierarchy. When creating additional animations, it is common to remove the skinned meshThe main graphics primitive of Unity. Meshes make up a large part of your 3D worlds. Unity supports triangulated or Quadrangulated polygon meshes. Nurbs, Nurms, Subdiv surfaces must be converted to polygons. More info
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from the fbx file. In that case the new import method ensures that the additional root node always exists and thus animations and the skinned mesh actually match.

If the connection between the instance and the FBX file’s prefabAn asset type that allows you to store a GameObject complete with components and properties. The prefab acts as a template from which you can create new object instances in the scene. More info
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has been broken in 3.4 the animation will not match in 3.5, and as a result your animation might not play.

In that case it is recommended that you recreate the prefabs or Game Object hierarchies by dragging your FBX file into your sceneA Scene contains the environments and menus of your game. Think of each unique Scene file as a unique level. In each Scene, you place your environments, obstacles, and decorations, essentially designing and building your game in pieces. More info
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and recreating it.