when the resources are in an external flash, they are embedded inside a resources file system (which is one of the multi application blobs that the DCT keep track of). Your application is not part of this file system. When updating your application, the resources file system is still intact and your new application will access it in the say way as the old application.
To update the web pages and resources, you then need to update the resources file system itself. This is done in almost the same way as updating the application. Recently, Currently the OTA server allows only to update the main application, however recently I have posted a TFTP implementation with a snip to update any file in the Multi application frame work.