COBRAS does not create links to any external systems (including phone system connections, LDAP links, digital network connections to other Connection or Unity servers, VPIM attachments etc...). The help goes into a bit of detail on this - but the short version is that you may be migrating between systems that have different phone system configurations - you wouldn't want COBRAS wiping that out - regardless reestablishing connections to external systems is incredibly difficult to do smoothly anyway.
So you need to configure your Connection server ahead of time - make sure it's taking calls properly etc... and then import your data. The COBRAS wizard will ask you to map phone system associations from the backup to any phone system(s) you have configured on your new Connection server so everyone is linked up properly after the restore.
