Honestly, I do not put any of my files within FL Studio’s file structure.
I feel this is the safest way to protect yourself, as well as keep yourself organized.
I store my music folder in a cloud-service, and organized in such a way that makes it easy for me to manage all my music files from projects to sounds!
So I would say avoid storing your files in My Documents, create your own folder and structure it the way you’d like. For backing up, make sure to have a local system in place, like USB drives with a backup software, as well as a cloud service for duplicate backups (redundancy), and you will never have to worry about missing files, or anyone touching your files 😉