In our ICN (3013) system, we have custom code which internally uses slightly elevated permissions to make changes to our Category or County columns. After the code is invoked, if Copy Link, or if the user uses the Favorites Folder view, the documents are no longer visible. It appears that this is caused by an internal cache retaining former values, and it was not noticed by the system that the Category or County columns had been changed. Is there some kind of method call that could be added to our ICN custom code which could force the flushing of this internal cache, so that the newly updated values can be re-acquired?

I would think you may add ?debug=true and debug the document properties modification save action. It will show how ICN process modification and reflect to the internal cache. All items have their own dojo object of contentItem to store data. I'd guess the corresponding ContentItem object data may need to be update.