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Our team has the same issue. Most of the time a restart solves it, but could randomly happen again.
Additionally, it also happens when I do changes on prefabs, they don't get updated on the instances in another prefabs (until unity restart).
Any news on this? This is really a showstopper for our save system. We're working with version 2019.3.x.
@DavidGeoffroy Any news on this issue? Since it still doesn't seem to work in Unity 2018.4. Is there a case number in the issue tracker?