The circumstances in my situation, which I just posted moments ago, are quite different, involving a module and a parent app.
But the symptom seems similar: deleted queries still being referenced in a strange manner: from a parent app that should be pointing to the Live version of a module where those same queries still exist.
Just thought I'd mention it as I was looking for something in the forums that might've been the same as my issue. Please ignore if this sounds unrelated 