WebOffice author provides support if your data frame(s) layers change during the WebOffice 10 R3 project life cycle.
If you navigate to Map collection in your project configuration then a button
is available on the right hand side of the Data frame property. By clicking the button it is possible to import the layer references from the data frame again.

Import layer references button in ArcGIS Server Map Service element
Choose the correct data frame and start the layer references import by clicking the Apply button.
Note: Information has been added to the ‘Import layer references’ dialog to make the administrator aware that it is necessary to have opened the underlying ArcMap document used for publishing the ArcGIS Server service for which the layer references should be imported.

Import layer references dialog – ‘Service name’ property and ‘Data frame’ information in import dialog must match