Reverting is not something Calibre can do.
Do you have a Sync enabled on you Library folder?

Run Library Maintenance Utility now, you have a mess because the DB says one thing and the books PATH may be something else.
Did you happen to click the Brown book icon in the Metadat Edit window. That reads THE BOOKs metadata. (or you ticked the 'Set metadata' in MDE Bulk mode)