Calibre arbitrarily removing my books

I am using Calibre 2.58 on Linux Mint Cinnamon 17.2 64bit.

I have just over 1000 books in Calibre and I noticed at times I go to find a book and the book is no longer there.

I have to re-add the book from my stored Bookfile. The last time this happened was last night and I had only added the book to Calibre a few months ago.

I really can't recall if this ever happened when I had Calibre in Windows.

Any suggestions, please and thanks?