In my 2018.3.12f1 scene I have a "button" prefab, and a control panel prefab. I drag several button prefabs onto the control panel, and then i drag the control panel to the assets folder and drag it back out into the scene a few times. Then I exit unity and start again. Mysteriously, all of the buttons are no longer prefabs. The control panels still are, but the buttons have unpacked, and of course a change to the button asset no longer appears everywherre there is a button. I have tried the same thing in a fresh blank project and it does not occur, only in my main game project. The hierarchy is somewhat more complex there, and I use scriptable objects liberally between prefab instances, if that might be the cause?