Importing sets settings in the associated .meta file.
Creating a prefab creates settings in the prefab and its metafile
Putting stuff in a scene gets saved in the scene.
Almost all parts of those things are connected via the .meta files.
As you work, be sure to use source control to track your progress and give you an easy way to back up when something goes wrong. I personally use git, but using anything is better than nothing. If you want pointers setting git up, say so and I can post my notes.
Meanwhile, here’s more info about Blender3D and Unity3D:
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, unwrap your UVs, bake textures if you must (like for AO), but always set up the materials within Unity and disregard what gets imported.
Costs of using Blender files directly vs exporting to FBX: