I appear to have fixed my workflow using this PDF Reader Pro Free application instead of Preview:
It enables me to delete and rotate pages and they are saved back to Evernote without the issues currently present with Preview.
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.