I tried once again and I was able to reproduce this time. The reason why it worked the previous time (thus my previous post) is because a prefab instance was still saved in the scene and apparently that helped in avoiding the problem for some reason.
After a few hours of looking into the problem, I got a few leads related to the json UnityObject serialization handling. Unfortunately I am still not able to fully fix this, but a fix is of course something that needs to be done. I just wanted to let you know that I am looking into this and I will update you in this thread as soon as I have a solution.