Layers get identified by the so called Layer identifier. The Layer identifier can be made out of:
•data frame // layer name
•data frame // top level group name
•data frame // top level group name // layer name
•data frame // top level group name // group layer name
So if the map document contains multiple group levels in the table of contents, only the data frame and the top level group layer name are saved in the layer identifier together with the layer or group layer name. Therefore, it is possible to assign identical layer names or group layer names in two differing top level group layers. On the other hand group layers of lower level will NOT be considered in the layer identifier. This is the reason why unique layer names or group layer names are necessary in differing group layers of one top level group. See the screenshot below for details how layer and group layer nomenclature will affect the formation of layer identifiers. On the left the original table of content is displayed, on the right it is possible to see which layers would have to be renamed because of identical layer identifiers.


Layer identification in WebOffice 10 R3 - Identical layer or group layer names are only possible once per top level group
The reason for identifying layers this way (instead of referring to the Table of content-position dependent ArcMap layer id) is that you do not have problems when moving layers within your map document.
Whenever the Layer identifier changes, WebOffice author updates the changes.
Note: Whenever you change the ArcMap document, the related WebOffice 10 R3 project should be opened with WebOffice author – otherwise WebOffice author is not able to update Layer identifier changes correctly. After changes have been done, ArcMap document changes as well as WebOffice 10 R3 configuration changes need to be saved.