As others have questioned, what site do you use which does not carry over lineups? Also, if that truly is the case, was it common knowledge? Again, if true, does the site allow you to set future week's lineups?
I have played at CBS, Yahoo, another I can't remember and currently Fanball. All carry over rosters. Altho answers to the above questions would impact my response, I would tend to think you should carry over his roster without regard to injuries and byes. That said, if he should have known they don't carry over and/or you can't set future lineups give him the goose egg, he earned it.