You can't fix that, because FAT32 does not allow symlinks.
You could only move the folders on your USB stick and reconfigure /opt/piratebox/conf/piratebox.conf that upload-directory is your moved folder (config file is commented)
You could only move the folders on your USB stick and reconfigure /opt/piratebox/conf/piratebox.conf that upload-directory is your moved folder (config file is commented)