See post from mkx: http://forum.mikrotik.com/t/capsman-config-cap-how-to-use-a-channel-list/138456/1
It is possible in Capsman to specify a frequency list which needs to be used, hence avoiding this major destruction 
Something like (2.4GHz example, user exercise to transfer to 5GHz )
/caps-man channel
add band=2ghz-g/n control-channel-width=20mhz extension-channel=XX frequency=2412,2437,2462 name=channels24
<channels 1, 6 and 11>
And then let it select auto from this list like
/caps-man configuration
add channel=channels24 name=net-2.4G <the rest of settings, e.g. SSID>
/caps-man provisioning
add action=create-dynamic-enabled master-configuration=net-2.4G radio-mac=E6:8D:8C:49:EE:4A <optional slave-configurations=>