There are no “mesh files” from a standard Blender import. Unity imports a Blender file as a series of different assets depending on what you put into it in the first place: GameObject, MeshRenderers, Meshes, Materials, etc.
All Unity does when it imports a blender file is call the Unity-BlenderToFBX.py script (located in your installation of Unity) and imports stuff.
If you recently upgraded Unity, around Unity2019 or so, they changed what they imported, so it will reshape EVERYTHING in your imports and break 100% of your prefabs if you have extra things like Camera and Light in your blender files.
Is that what happened?
If so, you can easily tweak the import script back to the way it was before, changing the one that Unity installs. You’d need to sort out any permissions to edit the file with your operating system.
There is a line in the above python file enumerating what will get imported. Make that line look like this:
exportObjects = ['ARMATURE', 'EMPTY', 'MESH']
Then reimport all and it should be back to the way it was before the upgrade.
ALSO: USE SOURCE CONTROL! 