I upgraded a site from 3.2.2 to 4.9.4.  After upgrade, many of the xml/xsl modules (60 or so on the site) no longer has xls as mapped prior to upgrade.  This may be due to this http://www.eguanasolutions.com/DNN_Blog/EntryID/1.aspx issue but I though I would note here since it appeared to be something else at first.  The module settings table showed all the correct mappings nor did the file ids in the files table change.  I actually do not know where the db field value was changing to correct but I chose to visit each module and reset xls source manually.  It was probably the shortest path to problem correction.