For a clone of Monero in a production environment, what files/directories to be backed up and and what intervals?
Once you have lots of people using your cryptocurrency, you can back up nothing at all (I'm talking about not backing up your seed nodes. If you have a wallet, you'll want to keep the mnemonic seed for that backed up, of course. And you'll want to keep a safe copy of your passwords/private keys that are used for connecting to the server via SSH and for logging in to your server hosting provider and domain name provider).
The whole point of a distributed cryptocurrency is that you all keep a copy of the blockchain, so that there is not a single point of failure.
This means that you could restore your seed nodes from the other nodes on the network. You'd just have to keep a note of some of the IP addresses of other nodes, so that you could reconnect your seed node to them when you reinstall your seed node after a disaster. Or better, you should encourage lots of people you trust to control their own nodes, who are willing to be listed as a seed node. Now you have resilience and don't need to keep your own written notes of IP addresses.
If you wanted to keep a copy of the blockchain on a machine that you want to control, just install a node on that machine, and it will constantly effectively back up the blockchain as it syncs with other nodes constantly during the day.