Here's a work around. Tag all the notes you want moved. Tagging doesn't give you the annoying dialog box. Scroll down on the left and view all the notes that are tagged. Moved all of them at once to the appropriate Notebook. You'll only get prompted once.
I just got a scanner for Evernote and this was immediately annoying. Give this a try on a Mac: Right click and open with Preview In Preview - select the page Rotate the page accordingly Save the change This appears to save it back into Evernote. This will get annoying with large documents.