So after all these days your Clip Sport is still not properly playing all the audio files on your SD card? Really sorry to hear this news…
I do know that the Clip Sport will automatically create a new MUSIC.LIB file on a newly formatted SD card. Also, the Clip Sport will automatically recompile the MUSIC.LIB file each time you eject the player from the USB port of your PC.
I always use the Eject Icon in the “show hidden icons” area of my Task Bar (Win 10) after I have copied files into (and out of) my Clip Sport. This gives the player a chance to complete all file transfers and then recompile the MUSIC.LIB file.