I'm beginning to get an inkling of what might be going on here: I've been bitten (mauled) by feeping creatures that I didn't even know existed. Apparently, Preview keeps a TimeMachine-like database of documents' histories. And I suspect mine is corrupted.
Until you mentioned the Opt-File/Save As... menu item, I had never known of it. The keyboard shortcut (Cmd-S) to "Duplicate..." is the same as the old "Save As...", so I figured it was just a synonym for the same behavior. However, I very rarely used it; instead, preferring Finder's "Duplicate..." (Cmd-D) if I needed a fresh copy (e.g., for backup purposes).
Suspecting my running version of Preview was fubared, I decided to close it down and restart. (BTW, I hate doing this, because all of the nicely tab-grouped windows I've setup are shattered into individual windows for every document when they are reopened. Not like Safari tab-grouped windows are remembered and repopulated upon a close/open cycle of the application.) But first, of course now suspicious, I wanted to check that the edits of each document had actually been saved correctly. The first open document I examined had a black dot in the center of the red button of the stoplight trio in the upper left, indicating that I had unsaved changes. So I typed Cmd-S; the black dot disappeared; but, curiously, the "Date Modified" entry for the file in my (Desktop) Finder window (sorted by descending "Date Modified", so it should have been promoted to the top) did not update to the current date/time stamp; the file I had just "saved" still had the three-day-old Date Modified. WTH!
It was then that I started exploring the various "save" options and discovered the TimeMachine-like feature (using "File/Revert to>"). I don't know what Apple intends for this versioning chaos feature, but it's broken, and should be withdrawn until it works more reliably.
Meantime, I struggle to "save" a version of the file that I can see on my screen...but can't capture into a disk file. I may have to sacrifice all of the edits in my current session and just close/open the application. Probably reboot, too, while I'm appeasing the Apple developer bit-bending gods, and further disarraying the current state of my Desktop (e.g., window placement within multiple Spaces...I use 12, across two monitors)
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When I get this squared away--or just give up--I'm going to explore another Preview behavior that I've experienced: crash after accidentally moving a graphical element (e.g. a "line" segment) off of the page. But that'll be a fresh thread ;-)
