I had the same problem where Beersmith acted as though it was a new install, and all my recipes were gone! All the files were fresh and new, even the archive files. I have now figured out what happened, at least in my case, and I have recovered everything.
I am using Windows 7, with a separate user account for my homebrewing, and use Remote Desktop most of the time. Something happened to corrupt the user account, and Windows was logging in with a "temporary user" account. It acts like the normal account has been logged in, but creates a temporary user, complete with the temporary files and directory structure needed. Once I figured out what was happening, I was able to navigate and find the Beersmith files in C:\Users\"username"\Documents folder. If you just go to "My Documents", Windows and Beersmith are actually using C:\Users\Temp\Documents.
Hope this helps a few of you with missing recipes.
-Jimmy