I am in the same camp as Dr. Ohh. What you experience is NOT NORMAL
I started using calibre shortly after I joined MR. I have done just about EVERY update on my XPpro system. I have never lost (track) of a Library in all those updates... Even the ones that failed (they were flawed and there have been a few of those.
Just part of the effect of being an early updater 
).
I/Me/Myself have done some
things that damaged Libraries, but it
never happened during an update.
The (Last used) Library location is stored in a (normally) hidden,
PER-USER, settings folder on every OS. Even if you UNINSTALL Calibre, this folders contents remains.
Something
else is in play here. A rogue
system cleaner? Logon as a different user?
Please say you are NOT keeping the Library on a Network share/NAS. This is not supported because it is NOT dependable for the type of use that Calibre needs