Changes to gameObjects not being saved in hierarchy

So, basically I have a few GOs and I simply move them(change their parent) click ctrl + S or Save Scene and then when I reload the scene the changes are gone. I find the gameObjects the same place they were in the beginning. Why?

If you didn’t understand what I wrote or just want to see it - Video example

So the problem was that the prefab of the gameObject was gone. Once I broke the link to the missing prefab it got alright. Yet I don’t see any logical reason why would this prevent me from moving the gameObject in the hierarchy?