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We are currently running 9.0 M080 and I ran the Remove Unreferenced files option last weekend, and it deleted a number of referenced documents too. The cutomerbulletin says that only 9.1 is affected (http://www.ptc.com/appserver/wcms/standards/freefull.jsp?im_dbkey=108272&icg_dbkey=222) but it affected us too. Watch out if you are on 9.0
Regards,
Rajesh Balasundaram