We are having this problem too. It is a quite serious problem since we cannot be constantly checking that all our prefabs are not missing their references with each commit... This issue should be addressed, for what I'm seeing, it has been reported since 2021 and looks like there is not a solution for it...
Missing references and .meta appears randomly when switching branches
in Unity 3D
Posted
We are having this problem too. It is a quite serious problem since we cannot be constantly checking that all our prefabs are not missing their references with each commit... This issue should be addressed, for what I'm seeing, it has been reported since 2021 and looks like there is not a solution for it...