Just confirmed the dnf system-upgrade probably does a rm-rf on the "download" dir.

From dnf-plugins-extras/plugins/system_upgrade.py:

=======================================================================
def clear_dir(path):
    if not os.path.isdir(path):
        return

    for entry in os.listdir(path):
        fullpath = os.path.join(path, entry)
        try:
            if os.path.isdir(fullpath):
                dnf.util.rm_rf(fullpath)
            else:
                os.unlink(fullpath)
        except OSError:
            pass
========================================================================

Guess what dnf.util.rm_rf does !   I'm guessing #rm -rf !  Which explains where my home directories went !

This is crazy coding !