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Final Cut Pro 10.1 includes some major changes to the inner workings of the app, including the addition of libraries for managing projects and events.
The locations of your libraries are stored in the preference files, so after trashing preferences with Preference Manager you may not see any projects or events after relaunching FCPX. This will also occur after using other tools that rely on Preference Manager such as QuickFix.
To get them back, go to File > Open Library > Other > Locate in FCPX and browse for the library files on disk.
Our recommended workflow for all applications is not to trash preferences, but to instead preemptively backup the preferences when they are stable and then restore the backup when things go wrong.