Well, I just tested it, and deleting iterator.pickle wipes away all bookmarks for me. Confirmed
and thanks for encouraging me to field-test my theory.
But you do need to make sure it is not being saved inside calibre_bookmarks.txt
If either one is present, the bookmarks will still be there -- and they will get updated in both.
You can stop calibre from saving calibre_bookmarks.txt in the Viewer preferences
General ==> Miscellaneous options
Uncheck "Keep a copy of the bookmarks/current page inside the ebook file, for easy sharing"
...
Yes, my example was a fragment of iterator.pickle
