Assuming the user has a Collab-enabled project, that his first commit has been done and that the scene contains prefabs with exposed components referenced.

N.B.: This issue was originally reported by user @pakfront on the following thread: https://forum.unity3d.com/threads/collab-losing-references-between-existing-prefab-and-new-prefab.458297/#post-2977977
N.B.: The following is a surefire way of reproducing the issue, but alternative repros exist. Fixing will need to account for edge cases around this type of function.

1. User 1 creates a prefab (Called "OtherThing") and attaches a script that exposes a component (like a transform):
a) public Transform theOtherThing;
2. User 1 creates a second prefab ("OtherThing2") and drops that prefab into the newly created component field. Publishes.
3. User 2 updates
4. User 2 renames OtherThing 2, publishes
5. User 2 renames to original (does not rollback)

Notice that User 2 sees the component as "none" while User 1 sees "OtherThing2"

ALT repro suggested by user:

I have an update - we get this behavior when we edit a prefab within the "Project" view. Specifically when dragging a reference of one component of a prefab onto the object field of another component of the same prefab.
I noticed that this does not trigger a Collab diff, that is the Collab icon remains a green check box.