Hello, I have finally been able to track down the long-standing reference issue that has been plaguing us. Repro has been sent as case number 1154829
First import a prefab but not the code. Then import the code. The serialized references in the scene instances of ChildPrefab do not update. They will be broken, even upon restart. They can be fixed by reimporting the prefab, or by saving the prefab.
This is extremely problematic and has plagued us for MONTHS. A general scenario is that our artists will update their svn checkout (which contains only the assets) and then do the git checkout (which contains the code). If the artist refreshes before doing the code checkout this breaks things, and usually we have to resort to a reimport all. We usually just reimport all because having an engineer determine what needs to be reimported in our large projects is a waste of resources.
Currently our workaround is to make sure that code is imported first. This is the best we can do until this bug is fixed. But ideally unity would not get ‘stuck’ in an incorrect state when you refresh assets!