Link Reference and Bundle ID are 2 very different things...the Link Reference is set in the Project settings and is used as the URLScheme. This allows you to open the app using 'link reference://..." from a hyperlink or similar. The BundleID must match the signing certificates from Apple. Typically, you will have a unique mobile provisioning file for each app you are managing.For your specific issue, I think you need to make sure that the mobile provision file contains the same bundleID (or app ...

All articles need to be in a collection for them to be visible in the app. Include the article in the collection, but in its metadata check the box to hide it from the browse page. Then it'll be part of the collection, but not shown when the user sees the browse page.Neil