Itunes music missing from itunes after plex loading



My iTunes library has both music purchased from iTunes and music I have ripped from CD's. When I activated PLEX all of my songs appear in PLEX but not in iTunes. Anything ripped no longer shows when I load iTunes, only the purchased tracks. The only way to play in iTunes is if I direct iTunes to the location on my computer where the ripped tracks are stored I can then import and then play them in iTunes. Why did PLEX remove these tracks from my iTunes library? This has effectively made iTunes inoperable.