I've never run into that problem. I program the primary & alternate CC channels and keep it updated weekly.
Unless it's a Harris P25 system in which case any frequency used by the site can become the control channel. Some Harris systems rotate the control channel through all the sites available frequencies each night at midnight. That can be frustrating for those that may have only programmed what they thought was the primary control channel!
Our local power utility rotates the CC every few days between maybe two or three of the available frequencies out of the seven or eight frequencies used by the site. They used to rotate the CC each night but changed that to a random amount of time.
The DB Admin for this area marked all the sites frequencies as Control Channels so the software that can ignore voice channels still downloads all the frequencies.
Harris systems also don't advertise any Alternate CC's either. At least I've never seen a Harris P25 system advertise alternates in the CC data.