I had a similar database database problem with my Clip+. I couldn't just add individual tracks, I had to drag the files over then rebuild the entire database which takes over an hour with a 25GB+ library. I had to clear the drive then reload the disk from scratch then rebuild the database again. Then I noticed a couple files were missing so I added just them, manually had it update the database and it seems to work now.
Patience seems to be the key. When you rebuild your database, set it going, connect it to a charger then go do something else for a couple hours to give it time to complete the task.
Oh, and a note to those working on the Clip+ code, make it update the database in the foreground because you can't do anything with an incomplete database anyway. If there was a display element to show progress that would be extremely helpful. I'm not a coder so just take this last part as a suggestion
