Hiya - I just ran into this in another app and I think I found root cause. It seemed like a permission thing so on a hunch I peeked at the local.meta and default.meta. The default.meta for the app had a bunch of stuff in there from the app being built. I removed all of it except the default and view stanzas, restarted, and then I was able to delete the input no problem. So I'm guessing there was some default.meta stanza made by a user not in my system that blocked my ability from deleting. If you got the app from Splunkbase then let the author know so they can clean out that default.meta.
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