Itunes deleted all of my music (CDs, non-itunes mp3 purchases) except for what was bought on the store

Today I was listening to my itunes collection on shuffle when I decided to restart my computer. I closed itunes and right before it exited a popup read "now saving itunes library" upon the restart I found that itunes had deleted over 2,000 songs that I had in my library that were from CDs and other medium not purchased on the itunes store. How is this even allowed? And how to I get my music back? Thanks anyone for their time.