https://issuetracker.unity3d.com/issues/prefabs-references-are-lost-when-modifying-prefab So, this is marked as fixed, but judging by the comments; it isn't, really? To quote somebody in there from Feb 3; "I investigated this a lot to find a workaround, and reached the conclusion that the new prefab system does a terrible thing: each time a prefab is saved it is now actually recreated, not updated. That means that, while serialized references are kept (GUID based), normal references are lost. It is really, really bad." Basically: this is horrifying, lol. We want desperately to upgrade our project to 2019.x from 2018.1, but this bug in particular also breaks 2DToolkit, which our project is dependent on. But judging by this bug, it could break much more than that, too. Do we have an actual up-to-date status on this issue? Is it actually fixed? It seems like the sheer amount of potential project breaking potential here should make it a top priority. Edit: my bad, 2018.3.6f1, where the fix apparently is, actually hasn't been released yet. 2018.x releases in 2019 confused the heck out of me.