There is the steps you can follow;
1. Remove Child site(If exist) server roles which connected to Primary Site you want to wipe out (https://technet.microsoft.com/en-us/library/bb632379.aspx )
2. Remove Child site(If exist) record from CM Console (https://technet.microsoft.com/en-us/library/bb632423.aspx )
3. Remove remote site system roles (like standalone DP,MP,SUP role installed on remote site systems) from servers which connected to subject Primary Site (https://technet.microsoft.com/en-us/library/bb632379.aspx )
4. Remove all removable roles from Config Mgr Console from Primary Site server (https://technet.microsoft.com/en-us/library/bb632379.aspx )
5. You need to remove old server machine account permissions of AD Container “DomainName\System\System Management” (https://technet.microsoft.com/en-us/library/bb633169.aspx)
6. Remove objects in System Management container belong to old ConfigMgr site/sites(If there is child site exist you need to delete those objects also). All objects in container which contains Site Code of old CM Installation you can remove safely. For example, if your old site code is PRI you need to delete below marked objects.
(If you accidentally delete a wrong object it will appear back in 1 hour but no need to take risks.)
7. Stop the services SMS_Executive, SMS_ComponentManager and SQL server on old primary site servers.
8. Push ConfigMgr2012 agent to client computers. Please be sure at least one Client Push account has been defined in ConfigMgr2012 console and this account Local Administrator on all clients. Using a domain administrator like below seems like shooting a mosquito with tank. Only local administrator permissions enough on clients and non-DC servers. By installing new agent to client computers, agents going to start report to new site code.
9. Check the Site Code in agent interface and registry value in HKLM\Software\Microsoft\SMS\MobileClient\AssignedSiteCode if the correct site code in newly installed clients.
10. Stop the data gathering jobs under Administration>Migration>Source Hierarchy if you are migrating objects from old installation. (See https://technet.microsoft.com/en-us/library/gg712313.aspx#BKMK_SupportedMigrationVersions for supported migration scenarios)
11. Please check the group policy if WSUS server address setting up by GPO. If it is update the GPO to target new WSUS server otherwise you don’t need to set a WSUS Address in GPO because CCMAgent Going to set up for you on each client .( https://technet.microsoft.com/en-us/library/cc720539%28v=ws.10%29.aspx )
12. On WSUS server of CM12 environment open IIS Console and navigate Server Name>Application Pools>WSUSPool thank click to “Recycling…” (There is another menu Item in same side pane as “Recycle” please don’t confuse them) and empty check box of Private Memory Limit. This is required because new installed CM12 clients will rush to WSUS after client installation for scan software updates and default 1.8 GB memory limit will not be enough to operate WSUS application pool for first day. At all we are always recommending remove the limit for WSUS application pool. Defining a memory limit is up to you.
13. “It’s now safe to turn off your computer”. Please shut down all old site systems but keep them for a couple days if you need any content or information from old servers.
14. After operation completed If you need migrate an old object from old site server to new installation only you need to start SQL server service on old database server.