Nested Prefabs unpack themselves when exiting unity

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?

 

It's possible. Can't really say from the details provided. We don't have any bug reports about Prefab instances getting unpacked by themselves after restarting Unity, as far as I'm aware.

 

How might I investigate further?

 

One approach could be to start with a copy of the complex project where the issue reproduces, and gradually strip it down to something simpler, trying to reproduce the issue many times along the way. Hopefully this will lead to discovering which element makes the different between whether the issue reproduces or not. You can then hopefully better determine if it's an issue in your project, or in Unity itself.

 

Cant be an issue in my project, im just using prefabs and doing nothing weird. There's a Unity bug in there somewhere.
Is there radical differences in prefabs in 2019? I am thinking of testing that out soon, it might be an alternative

 

Well if you know it's a bug in Unity, then I'd suggest submitting a bug report so we can look into it. But there's a higher chance we'll have time to investigate it and fix it if it's a minimal project rather than a large and complex project with lots of elements that might not be related to the bug.

There shouldn't be a radical difference in Prefabs between the latest 2018.3 release and one of the 2019.x releases, except you can't edit Prefabs root GameObjects from the Project view (yet).