Asset DB v2 does not restore metafile the same way v1 does. I think the v1 behaviour is desired, but should be determined before fixing this case.

Repro steps

1) Create a material - "test.mat"
2) Add a label to material - "test.mat"
3) Save project
4) Open "test.mat.meta" and see label set in meta file
5) Delete "test.mat.meta" outside of unity
6) Give unity focus to trigger refresh
7) Open "test.mat.meta" again and see that label now is missing in metafile

When asset db v2 restores a metafile, it doesn't restore all previous values. It only restores the GUID. V1 restores all values.