All persistent data should be stored in the JADE database. You should consider at risk of full or partial loss any data necessary for the operation of the solution that is represented in the form of non‑database files (flat files), and you must be able to be recreate those flat files somehow, whether that be from the JADE system itself or from an external system or user.
If there are compelling reasons for the application to maintain data in the form of flat files external to the database, you must be mindful of maintaining both integrity and performance.