Geralt loses his (steel) sword in the cutscene at the end of the fight. It does not automatically go to your inventory, but you should be able to find it on the floor. I'm not sure why you're not seeing it there. Perhaps you have to pick it up right after the fight, or maybe?
Edit: I just played through that part again and it willseems that the sword on the ground is not be hightlightedhighlighted by the medallion?. You'll have to look for it yourself.