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!
It is not in the Calibre preferences but in the Viewer preferences. Open an ebook in the Viewer and while in the Viewer press ESC to get to the menu, then the option is under Miscellaneous.
That behaviour was for the old viewer with version 3. The new version 4 one reverts to what GP is saying: you have to open an ebook before you can even access the settings through pressing ESC or right click.
Also the version 4 ebook viewer is step back from the old one, as it stands now. It is slower, more resource hungry and buggier. The only arguable improvement is it now uses a 'flat' theme that doesn't look dated. I'm even considering reverting back to Calibre 3 because of the ebook viewer randomly freezing on large epubs with equations and so on.
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!