Here’s a quick note on a new hotfix we released in case you run into the problem. When a service window is created on one site in a System Center Configuration Manager hierarchy, service windows on the other sites in the hierarchy may be deleted. For example, after you create a service window for the Central Administration Site (CAS), a new service window is created for the child primary site, however after a second service window is created, the first service window that you created for CAS may be automatically removed.
A supported hotfix is available from Microsoft Support that addresses this problem. For complete details please see the following:
Note that after you install this hotfix each site can have its own service window, however previously deleted service windows will not be restored.
J.C. Hornbeck, Solution Asset PM
Microsoft Enterprise Cloud Group