Zimbra Migration tool saves the imported items information in local machine from which the migration tool is been executed so if you delete the account from ZCS server, it is not going to make difference. Please unselect the 'ignore previously imported item' option for running the migration tool multiple times to migrate items in complete once again.
Zimbra migration tool log files are stored at C:\Documents and Settings\<profile_name>\Local Settings\Temp\ZC***change<version> .