System Information
Intel i9-10850K, 32 Gb RAM, NVidia GeForce GTX 1070 8GB
Windows 10 x64

Blender Version
Broken: 3.x
Worked: 2.9x

Short description of error
When you Link something that contains Vertex Groups to a new scene and make that object local while leaving its data either linked or overridden it loses its vertex groups after you reload he file. I have noticed another very peculiar thing – if you link the same object again, vertex groups will magically appear on previous object as well and will stay there until you remove the linked object from the scene. I'm aware about Blender's issues with Vertex Groups but this is different because the same exact thing doesn't happen in 2.9, perhaps this is the result of the refactoring done in https://developer.blender.org/D11689 ?

Exact steps for others to reproduce the error

1. Open Blender and add a Vertex Group to a Cube, save.
2. Open another Blender and Link the Cube from the previous file.
3. Make Cube object Local while its Data should stay linked or overridden.
4. Save and reload the file and you will see that Vertex Group on the Cube is gone.
5. Link the Cube again from the previous file and Vertex Group will appear on both Cubes for some reason. If you leave the second Cube in the scene both groups will stay, if you remove the linked Cube the first Cube will lose its groups after reloading as well.

Or:

• extract .zip somewhere
• open T94424_main.blend
• with the selected Cube: Object > Relations > Make Local > Selected Objects
• save and reload the file: vertex groups are gone