Well, that is a new one on me. Smart Content can go away if the CMS is not running, but the Content Library should always display the content as it appears on your HDD.
DS4 uses the paths given in Edit > Preferences > Content Library > Content Directory Manager to populate the Content Library. What do you have in there for DAZ Studio Formats and Poser Formats? Have you recently changed anything in there?
Can you post a screenshot of the collapsed listing for both DS Formats and Poser Formats please?