I want to do a Bare Metal Backup of my server but I'm concerned about opened files.
My server contains many SQLite databases, and SQLite daemons are active 24/7/365. As I know, you cannot backup a SQLite database, while the daemon is active, by simply copying files, otherwise the backup will be corrupted.
I know some Bare Metal backup tools offer specific agents for some types of files, but no one offer agents for SQLite.
How the Bare Metal backup deals with opened files and with write cache?
There is a SQLite backup API available for command line scripting. Previously, backup scripts tended to get locks preventing writes while doing their copy.
Being able to snapshot the storage, either LVM or otherwise, also helps. Suspend writes long enough to take a snap, then copy off the no longer changing snap at your convenience.
This pattern is not unique to SQLite or bare metal. Quite a few kinds of databases should be quiesced while you take online backups.