When I re-position (with Transform) a few layers so some of them are physically outside of the artboard, all of the layers I have just moved are "kicked out" of the artboard (thus also moving them out of their current layer hierarchy).
That's probably because when you repositioned them, it forced that element outside the artboard, which is going to kick it out of the artboard and throwing it off of its current Hierarchy. In my graphic design work, I am sometimes working on files that have several artboards and I have that happen more often than not.
There's a hard-to-find setting for artboards that should fix this and other wacky auto-heirarchy-changing artboard behaviors:
1. Select the artboard tool specifically from the tools panel. 2. Select the options gear icon in the tool properties menu at the top (right under the main app dropdown menus) 3. You should see several artboard options. These are saved per-document like print settings so you need to re-set them for every new document. 4. Uncheck "Auto-nest Layers". If this option is enabled, the artboards try to grab or eject layers based on how much of that layer overlaps the artboard. It is on by default. 5. I also recommend turning on "Shrinkwrap Canvas on Save" so it will crop the canvas size back in to minimal size.