It seems that you have the IP phones used by your IPCC agents registered to the publisher CallManager server and no failover CallManager is configured for them, so when you shut down the publisher, the ip phones became non functional. The ip phones are only "dummy" devices: all call processing is done on the CallManager server so, if that server is off-line and no failover server is configured, the ip phones are actually dead.
In order to configure a CallManager failover server for those ip phones, please do the following:
Open the CallManager administration page > go to the "system" menu > select "Cisco CallManager Group" > at the new displayed page, click on the link "Add a New Cisco CallManager Group" > at the "Cisco CallManager Group Configuration" page, enter a name for this new group at the field "Cisco CallManager Group" > leave the "Auto-registration Cisco CallManager Group" checkbox unchecked > under the "Available Cisco CallManagers" list, you will see your publisher and subscriber servers > using the arrows, please move first your publisher server to the "Selected Cisco CallManagers" list, then do the same for the subscriber server. Click on the "insert" button at the top of the page.