Not sure if you’re using Blender or how you’re getting stuff in, but if you restructure an FBX / Blend file, you can expect almost 100% of what you do in Unity (prefabs, scenes, etc.) to need a good looking at. This is because Unity “knows” the parts in your file by hierarchy name and you changed it, so stuff will be disconnected or reoriented.
Here’s my wall of random Blender3D and Unity3D integration notes… hopefully it can help you reduce friction in your workflow:
Costs of using Blender files directly vs exporting to FBX:
Unity imports Blender3D objects as FBX via a little Python script:
The Python script that Unity uses (substitute your Unity version number or search) to import:
Blender3D objects used as trees / detail in Unity3D terrain (See the second half of this response)
Probuilder and Probuilderize and Blender:
Some more potentially-useful info:
Updating Blender files without breaking your prefabs:
When I work in Blender3D for Unity3D use, I follow these organizational rules:
use Empty Blender Objects as folders: they come out as an extra GameObject
ALWAYS parent everything to a single Empty, even a single object
ALWAYS apply all Scales and Rotations on every Transform throughout your hierarchy.
put as few objects in a given .blend file as possible, combining them in Unity into a prefab
REMOVE unnecessary items (Light, Camera, etc.)
use good names for your Blender3D objects and NEVER RENAME them after Unity sees them
don’t even think about final Materials or Textures in Blender. Set the mesh to use N different materials, but always set up the materials within Unity and disregard what gets imported.