There have been several reports submitted to Apple, myself being one of those, with the problem. The issue rears it's ugly head when you restore a backup from an iPhone 5 to an iPhone 6s. You can set your phone up as a new device and reinstall all the apps through iTunes. But you will lose any data you had for the apps that is not stored in the cloud. (Calendar is OK for example). What you do lose are your email accounts on the phone that will need to be redone as will any wifi passwords. A significant effort for some people.
Apple is aware of the issue. It will not be fixed in 9.1, probably 9.2 before the issue is resolved.