This also causes an issue with Editing colliders in the Prefab sandbox. When in Edit mode on a collider's component, after you change a vertex on the collider if you have AutoSave enabled it will exit out of Edit mode.

ProTip - don't use AutoSave in the Prefab Editor.

Interesting workaround with the AssetModificationProcessor. Don't know if it's better or worse, but we found out that the AssetDatabase can still tell you things about the object even though it has become "fake null". So here is the solution we used in Odin for anyone interested:

private static bool ComponentReferenceIsBroken(T component, ref T realInstance)
{
var uObj = component;
var oObj = (object)uObj;

if (oObj != null && uObj == null) // Checks for fake null.
{
// It is safe to get the InstanceId, even though it's fake null.
var instanceId = uObj.GetInstanceID();

// The AssetDatabase still knows the broken object, and here it returns true if it's a reference to a prefab.
// If it returns false, then it could either be destroyed or just "fake null" as serialized unity objects often are.
if (AssetDatabase.Contains(instanceId))
{
// This parts gets the new reference from the prefab.
var path = AssetDatabase.GetAssetPath(instanceId);
var realWrapper = AssetDatabase.LoadAllAssetsAtPath(path).FirstOrDefault(n => n.GetInstanceID() == instanceId) as T;
if (realWrapper)
{
// And gives you the new reference.
realInstance = realWrapper;
return true;
}
}
}

return false;
}

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.
The best workaround I found is to use Unity's AssetModificationProcessor to store the path of the saved prefabs just before they are saved, then use an AssetPostprocessor to reload them from said path after they have been reimported. It's a delicate hell :|

Why is this not Priority 1? The tooltip for Priority 1 mentions "data loss" - this bug nulls out your references. It's entirely project breaking. It fundamentally breaks how Unity is meant to work.

2019.1 cannot ship with this, it's bad enough it made it to 18.3; it renders the new prefab workflow redundant for anything with a mono reference. Very sad, because nested prefabs are fantastic!

Please fix asap!

Same as @NONGBENZGAMES for me

Same as @NONGBENZGAMES for me

I too have references in other scripts going missing when updating prefabs. Components randomly get new FileIDs for some reason according to my Git. This has happened since the beginning of new prefab workflows to the latest 2019 alpha13. Not sure if it's due to a faulty upgrade process but this has been project breaking for months and needs attention.