Why does scaling during preflight not work on all documents?

You can create an Action with a script to "Save A Copy" and then save to a different folder.  It won't overwrite the existing file so you either have to change the file name, or save to a different folder.  The documents that were Reader Extended will be exact copies of the originals with the Reader Extended removed.  Those that weren't Reader Extended will simply be copies of the originals.  So you will end up with a new folder of all your documents and none will be Reader Extended.  You can then run your Action one the new folder.  Here's an example of the Action script to run on the folder of PDFs

//Here's an example of a path to the folder you will run the action on:
//"/C/Users/User/Desktop/Original Folder/Document1.pdf"
//Add another folder ("New Folder") for the output in the same directory as Original Folder (Desktop in this example)
//Use the following script in the action:

this.saveAs({cPath:this.path.replace("Original,"New"),bCopy:true});

//The script above is the only thing you need to do in the action.  Don't create another Save action.