I found the following issue in SQL DOC versions 126.96.36.199 and 188.8.131.522:
I had to update and rebuild a number of XSDs that are used to build a set of XML Schema Collections on a development server.
I used SQL Doc to generate a set of help files, one with the before image of the database and another after the change was made to the database. I created a project that contained only the XML Schema Collections, then I opened and used this project to generate the before image, made my changes and generated the after image.
The help file that SQL DOC generated had the original XSD content in the XML Schema Collections section for both the before and after image unless I closed and reopened SQL DOC.
SQL Doc makes it look like it is getting a current copy of the database schema while it is generating the help document, but apparently it only gets the current object definition at the time the project is opened.