I believe that I have it fixed. I selected a bunch of ePub files and did a drag/drop on the Calibre window. This apparently creates an alias of the file in Calibre Library (not a copy) so if you delete the originals Calibre gets understandably confused. I should have noticed the difference in the cursor between doing a simple drag/drop (alias) and holding the Option key down during the drag/drop (copy file).
However, OPDS doesn't work anywhere I tried it (Safari, Firefox and Chrome browsers on the desktop and mobileSafari on iPad 2). Looks like Stanza is the only eReader that still understands OPDS.
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