If your Papers library appears empty after recent changes to your computer, this usually indicates that Papers might have lost the information of where to find your library. You can re-associate Papers with the location of the library from the Library Preferences. The Papers library folder is located next to your Papers1 library by default (if you migrated from Papers1), or in /Users/[your_user_name]/Library/Application Support/Papers2 if you started using P2 from scratch.
You'll have to point out the location of your library again for
Papers from the Library Preferences tab by clicking "Change..".
Note that again if you use Lion or Mountain Lion, there might be an extra complication here in that the Library/Application Support/Papers2 folder which is the default location for your library is hidden by default. You can find it using the above steps including "Go" in Finder (use the "Go" menu in the Finder while pressing the option key (alt), which will add a 'Library' item to the list when you're in your home directory, then navigating to Library/Application Support/Papers2), and dragging the Papers2 library folder you see in Finder to the dialog in Papers2 Library Preferences tab after pressing "Change.." We're sorry that this is so complicated -- unfortunately Apple decided to hide the Library folder in Lion and Mountain Lion.