I was going to put a book on my Kindle and when I opened my Calibre library much to my surprise I didn't have one book in it.
Anyone know what happened
Not sure if this is your issue or not, but I've had this happen to me. I use the Calibre Portable program, on my external harddrive, and it seems to happen more often in this scenario.
For some reason, the Gui.json file (which tells Calibre where to look for libraries and books) gets corrupted. I now keep a backup copy of the file and just copy it back and that fixes it for me.
One of these problems could also be your issue: You are not allowed to view links.
. There are instructions on how to fix it
Hope this all helps!