To permanently delete a document from your iPad, follow these steps:
STEP 1. Make sure the document appears in at least one Document Binder.
STEP 2. Open up the Catalog view and locate the document you wish to delete.
STEP 3. Swipe your finger from right to left on the name of the document.
A red Delete button will appear on the right.
STEP 4. Tap the red Delete 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.