To answer your questions in one go, you can't automatically directly copy the full blockchain directory on a slave (connect only) node to the master node because each node has a different wallet and tracks different addresses.
So you have two sensible approaches to backup and disaster recovery.
The first is to share the private keys (and any watch-only addresses) from the master to slave using dumpprivkey, importprivkey and importaddress and then the nodes are effectively full replicas of each other. At any time you can stop one of the nodes, back up its directory, and then later that directory can be used to start up another node, between master and slave and vice versa.
The second is to only keep a backup of a node's private keys, and let it recover everything else from other nodes on the network (which could be within other organizations). In this case you recover a node by starting it with -initprivkey passing the private key of the address required for connecting, and then use importprivkey for the other private keys it should hold. Or even simpler, back up the wallet.dat file, and use that for restoring the node's wallet after which you run MultiChain with -rescan=1.
One important note: if two nodes are sharing a private key, you should not simultaneously create transactions for an address corresponding to that private key in both nodes. Use one or the other, and only switch if there's an actual failure. Otherwise you can get double-spend failures.