For reasons that aren't clear Apple only allow an iPhone to be manually managed with a single library. Occasionally an update might mess with the recognition of the current library causing it to be treated like a new library with respect to the device, or you might move your library to a new computer in a way that doesn't preserve this hidden identity. Syncing with selected playlists is a better approach as it allows you to manage what is scheduled to go to the device whether connected or not, and makes it much easier to put back the content if it ever needs to be restored or replaced.
With all that said I don't know why iTunes isn't listing the current content of the iPhone, unless it only has cloud references to songs in your purchase history. Since you cannot see them in iTunes, and iTunes doesn't allow content to be copied from a device to the library, I would try iFunBox and see if you can recover them before attempting to add any new content.
tt2