Sorry, I was travelling when you posted originally. :)
I have no idea what happened, to be honest. As for a solution, I would attach an external drive, log in to your server via remote desktop, and copy the files from C:\FS\etc. to the external drive. Then I would copy them (still on the server) to \\localhost\<sharename>.
If you're not certain what you're actually missing, copy everything from C:\FS.etc. and then back to the shares.
I'm not on the WHS team, I just post a lot. :)