I've ended up in this situation too. We migrate between datacenters with duplicate hosts fairly frequently at my primary place of employment, and best practice

I've ended up in this situation too. We migrate between datacenters with duplicate hosts fairly frequently at my primary place of employment, and best practice is to use the cname of the service to access the server currently acting as the primary for it (e.g. foo.bar.com as opposed to foo.datacenter.bar.com). That leaves me with a lot of foo.bar.com entries to clean out of known_hosts, or a lot of spurious MITM errors. What I've done is added a whitelist to my .ssh/config to disable the alerts only for those hosts. The foo.datacenter.bar.com address (which I use often enough, usually when migrating it between datacenters) still alerts. And yes, I know I'm living in the 90s what with my datacenters and whatnot. They're kind of like regions... what? Oh... why, you... You kids, get off my lawn!