WebOffice author provides some information in the status bar. The status bar is used for
•Providing version information of the currently used configuration scheme,
WebOffice author configuration scheme version
•Providing important user notification information, e.g. information on where an invalid configuration has been saved.
WebOffice author notification
If WebOffice author needs to update the map document because of e.g. duplicate layer names then it uses a small modeless window for showing this information, e.g. if an ArcMap layer National Capital Cities is dragged into the Cities layer group where a layer named National Capital Cities already exists then WebOffice author automatically ensures layer identification uniqueness. This is shown in the modeless window:

WebOffice author modeless notification window