To make quite clear my suggestion: If the front window was your home folder, then the Library folder could be selected by pressing L or by pressing arrow keys. If the ENTER key (bottom right) is then pressed, you begin to edit the name of the folder formerly called Library. If ENTER is pressed again, then the folder is renamed, and numerous settings become invisible to your applications.
Since this can all be done with keys at the bottom right of the keyboard (arrow, 0 and ENTER) it seems a likely scenario. The system would later recreate the missing Library folder, leaving the real Library folder named something like 0.00. If your son succeeded in naming it beginning with "." then it would be invisible in the Finder too. That would also be easy to do.
You will need to use Applescript or terminal.app to retrieve your settings in the invisible case.
To see your invisible files in the Finder, open terminal.app (in Applications>Utilities), and type:
defaults write com.apple.Finder AppleShowAllFiles YES
then restart the finder (option-click dock icon to select relaunch)
You would then see your renamed real Library
same trick with NO to hide files again.