I appear to have fixed my workflow using this PDF Reader Pro Free application instead of Preview:
https://itunes.apple.com/gb/app/pdf-reader-pro-free-all-in-one-pdf-office/id919472673?mt=12
It enables me to delete and rotate pages and they are saved back to Evernote without the issues currently present with Preview.
EDIT:
you can't delete more than one page at a time;
to re-arrange pages you need to cut/paste instead of dragging like and Preview;
to merge documents or insert pages it's a clunky process rather than the intuitive Preview drag and drop.