Playlist won't appear on itunes 11.3 when synced with ipod touch.

I like to download songs onto my iPod Touch (5th gen, 8.3) that are not on the iTunes store, but through iTunes software on my computer, but everytime I do this, some of my music files are gone, and an entire playlist is whiped of a majority of its songs. To makesure it doesn't happen, I created a backup file, which when I sync, doesn't appear.