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It's not always possible but it's generally good practice to configure your applications to use external storage rather than file systems - MySQL/PostgreSQL for indexable data, and S3-clones like MinIO for blob storage.
One major reason for this is that these systems generally have data replication and fall over redundancy built-in. So you can have two or more physical servers, have an instance of each type of server on each, and have these stay synchronized. If one server goes down, the disks crash, or you need to upgrade, you can easily rebuild a set of redundant servers without downtime, and all you need to do is save the configurations (and take notes!)
Like I said, not always possible, but in general the more an application needs to store "user data", the more likely it is it has the ability to use one of the above as a backend storage system. That will reduce, significantly, the amount of application servers that need to be backed up, and may reduce your need to consider using NFS etc to separate the data.
Interesting! I felt S3 was more a business cloud storage api.
I did a quick search, and it seems neither syncthing or jellyfin is compatible with S3. What do you do in these cases?
Rclone can do this for you.