Running your own server is cool, but having backups is a must in that case.
Here is how to do it for the EteSync server, but the procedure depends on your storage backend
Database
SQLite3 (with the default name given by EteSync)
sqlite3 /path/to/etesync/db.sq3 ".backup '/path/to/backups/backup_db.sq3'"
If you want more info https://stackoverflow.com/questions/25675314/how-to-backup-sqlite-database or check the SQLite3 documentation.
PostgreSQL
Basically just dump your database using pg_dump (here we assume the database is called etesync).
pg_dump etesync > /path/to/backups/etesync.dump
If you want more info https://www.postgresql.org/docs/current/backup.html
secret.txt
it's not required to back this one up to backup your data, but having a backup of this file will make it easier to restore the database to a new EteSync server. This secret is essentially only used for hashing the login password. So it's not essential, but probably good to back up.
cp /path/to/etesync/secret.txt /path/to/backups/