General "Undo" functionality and editing history
I'm brand new to AC and Unity and just starting to learn the tools so please forgive my ignorance 
. I'd like to know exactly how the "Undo"/changes history/and auto-saving works?
_Not sure if this is covered in some beginners resource or basic user manual, feel free to direct me towards that so I don't have to spam this forum with basic questions. _
Basically I was just messing around with the tools in a test game, making hotspots, adding inventory items, etc. And then I clicked to rename my scene in the assets folder. It asked if I wanted to refresh the scene, and not knowing what that meant, I clicked Yes. And then all my hierarchy items reset to default (except for the art I had place in the scene for some reason). All my hotspots were gone, the NavMesh I customized, my Nav Cam, everything just gone. And then I realized that there was no "Undo" for this. Ctrl+Z seemed to just jump between things I had previously selected but not revert any changes. I closed the game, reopened, and it seemed to have auto-saved because everything was still gone.
Luckily I was just messing around and no hard work was lost, but what exactly did I do wrong here? How come the Undo button didn't fix my mistake? I would hate to make this (or a different) mistake again and not be able to Undo it when working on a project that actually matters.
Sorry again for my beginner ignorance and thanks for any advice!
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I believe is because Unity does not like renaming of Scenes, could be wrong though!
Is this to say that the scene Hierarchy reverted back to an "empty" scene, i.e. just a camera and light?
I can only speculate, but my guess would be that it was reverting to the last saved-state of the scene file itself, rather than the state that the "live" scene was in. If Unity detects a name change in the active scene, it'll disregard unsaved changes when re-opening it.
It's good practice to play around in a test scene/project as you're doing, though! When it comes to your proper project, I'd always recommend the use of version control, as it's a much more reliable way of keeping track of any changes you make. If you're just starting out, I find that the most hassle-free option is Github Desktop.