There was a hardfork and your older miners didn't have the updated code to operate on the newly forked blockchain. Steemd.com gave the warning about the hardfork, and hopefully will continue to give people a warning in the future too.
You don't need to mess with the cli_wallet at all if you're only mining. And to transfer the encrypted keys for cli_wallet you copy the wallet.json file in the /cli_wallet/ directory.
Also you can add rpc-endpoint = 127.0.0.1:8090 in your config.ini if you need to access steemd from another program (like cli_wallet) and you won't need to use the switch from command line.
Thanks for the info. Copying the wallet.json file makes the upgrade process even simpler.