If a custom fields was added without including it in the Data Warehouse, can it be updated and the existing data pushed to the Data Warehouse one time?
Yes. The “Include in Data Warehouse” option needs to be updated for the object in Setup. Then the System Administrator will need to run the Global Search Index Tool if you want the fields included in Global Search, and then the DBA will need to restart the Data Warehouse and TeamConnect.
Is it correct that you can save over the default, out of the box reports?
Yes, it is possible to save over an out of the box report. A Best Practice is to save all of the out of the box reports into a separate folder and apply security to that folder. Then place a copy of the reports in a new folder for general use.