Same just happened to me. Update Manager came up, saying update available "Railclone" version 3.0.0.
I thought it was weird, since the I have 3.0.4b.
However this is of course a beta version, so I thought, maybe this was the final version. So I updated.
I then opened Max, to check the version number, only to discover all the libraries were empty.
Good thing I found this thread and downloaded and double clicked the reg file and now everything is back to the way it was..
Bit of a panic for a moment there, it would be great though, if you could figure out what went wrong, so it doesn't happen again