Your first scenario is different from the last one. In the refi scenario, you denied the loan so you can't make the argument that it wasn't an application....you denied it. In your 2nd scenario, i agree with TR IF you aren't taking any action on them prior to sending out an incomplete notice or denying them for being incomplete. If you are denying them based on anything else, then you're treating them as an application and they'd need to be reported IMHO.
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I'm fixin' to fix that.