I’m seeing two ways for this.
One – Upon the conversation starting between the flag and command, the flag would put out a very brief fleetwise message over comms that the flag is not to be disturbed. This message could either be a few words, or a sound. The same thing could then be done when the conversation has been ended.
Two – This one would cut down on the ever-present fleet-wide comms chatter. If the Hydra (for example) needs to talk to the flag, the captain would first hair the Comms officer with something like “TSN Hydra to TSN Raven.” The Comms would then inform the fleet captain that the Hydra is hailing them, prompting the fleet captain to contact the Hydra directly.