I don't know how it could have moved them. You choose itunes (Connect to iTunes) to receive the files for your iDevice (in the dropdown where the server item is... cant remember,.. nowhere near computer at the mo) and it plants them in your books library in iTunes. Then, you sync via itunes to get them into iBooks. I wouldnt know *how* to move them directly.
In any case, if you sync with itunes now, those books should now be copied to iTunes. Youll have to copy them out to a folder (or not, just tell Calibre where they are) and they will go back to your C library. As for the metadata... thats something you'll have to search out via the edit metadata dialog.
Whatever you did, this time, don't do it again! I'm puzzled about how you managed it.