To permanently delete a document from your iPad, first make sure the document shows in at least one Document Binder. Next, open up the Catalog view and locate the document you wish to delete. Swipe your finger from right-to-left on the name of the document and a red Delete button will appear on the right. Tap that button to delete the document. This will delete the document from all binders and remove the file from your iPad. This will also prevent you from getting updates to the document in the Downloads view.