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Only pages in /certaindirectory/ have been affected. Unfortuantely, those pages are where i keep the articles.
Something happened between 2-5am EST. I went to sleep fine. Woke up at around 5 and all pages were gones. Still listed with site: but they are all now the very last ones.
Good luck to all!
I've perused the forums a little today and it looks like some sites who survived June 27 are now having trouble.
My guess is that Google fixed or changed their algorithm again and/or did the other data refresh that Matt Cutts predicted would happen this week.
Have hope everyone, it looks like things may be getting fixed.
The site that has returned now shows up correctly for the site: command, while the other site shows up differently for the site: command that it did yesterday, but still not correctly. Maybe there is still hope it will come back.