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 ID) as the IPA you created.