Will PowerToys remaps persist after reboot, and are there steps if remappings disappear after restarting Windows?
Yes. According to the article, once you save remappings in PowerToys the new key mappings take effect right away and can be removed later via the app; this implies remaps persist. If remappings disappear after restarting Windows, undo and redo or reapply them by opening PowerToys, going to Keyboard Manager, selecting Remap a Key or Remap a Shortcut, and saving your remappings again (see How to Undo Key Remapping). Answered
Are there known limitations or specific keys besides Fn and Ctrl+Alt+Del that PowerToys cannot remap on common laptop models?
Yes. The article states that some keys cannot be remapped because they are reserved by Windows or controlled by hardware or firmware. It specifically mentions many laptop Fn keys and the system-level shortcut Ctrl+Alt+Del as examples that typically cannot be remapped. Answered