The initialisation wizard will ask you basic things like MWI DN, IP address of CUE, etc. thus will overwrite the existing configuration.
There is an option to skip the initilisation wizard though if you would like to keep your current configuration.
Kindly refer to this guide:
http://www.cisco.com/c/en/us/td/docs/voice_ip_comm/unity_exp/rel7_0/administrator/GUI/GUIadmin/init_wiz.html
Please rate replies and mark question as "answered" if applicable.