Can you provide little more detail about your desktop workbook data sources? whether they pointed to Tableau server data source or a local data extract?
What is your data source excel /Tableau data extract/ Sql server etc.. ?
If desktop workbooks are connected to local extract then you have to refresh them manually from desktop, else change the connection to Tableau server data extract.
Are the workbooks referencing the data connections as Tableau Server connections or are they using the original connection? If connected to a Tableau Server connection with an extract, that's the only one that needs to be refreshed. If the workbooks are using their own extracts, then those extracts will need to be refreshed too.