....Any idea how I can make LR show me which files it thinks are missing? Clicking on the number doesn't show any images.
I have done a quick test and clicking on the "Missing Files" filter I get displayed the images not found anymore (those with question mark).
You say also that you do not see any with question mark, I soppose browsing the entire library...
so, I don't know what to think...
some kind of db corruption?
Have you tried a Database Integrity check ?