Just updated. Alas, the new viewer still does not provide nondestructive viewing. Open file, press PgDn, exit, and the viewed file is silently changed. The viewer writes current position in the viewed file itself (META-INF/calibre_bookmarks.txt).
UPDATE: just found out there is now a checkbox in the viewer preferences: "Keep a copy of annotations/bookmarks in the e-book file, for easy sharing". If unchecked, the viewed files are kept intact. Nice!