Iapp template for exchange update, flush old application

The iApp only knows about the objects it creates and "owns" (which ones are tagged with the app-service property and live in the iApp's folder).

Sounds like someone came along after the iApp was deployed and configured other objects (either manually or using another iApp deployment) to point to its objects. When you deployed the second iApp, did you select any objects that were created by the first?

At any rate, you shouldn't need to modify any of the first iApp's objects to get it to delete. You need to look for the non-iApp objects that reference it and reconfigure them manually, or reconfigure the second iApp to create new objects instead of reusing ones from the first iApp.