Have you tried un-installing the Agent on the host computer and deleting the host in the MC? Then, you would re-install the Agent on the host. That will force the Agent to register with the MC, get all the new rules, and start fresh.
I get the feeling it's not responding because once those rules were downloaded to the Agent, it went into Lockdown mode (no traffic comes in or goes out), so that might include MC traffic.
Also, if you want to try enabling Rule 46 and re-enforcing the rootkit protection, I would put that Rule Module into Test Mode. That way you only see what it would do and it won't actually lockdown a host.