This is the first chance that you have to impress a coach. Show them that you are hungry for the chance to play baseball in college. Players should return all questionnaires to ALL schools that write them. Even if you are not interested in attending a certain school, still return the questionnaire they send you. You can simply write that you are flattered that they are interested in you, however, at this time your interest leads you to other opportunities.
All coaches talk to each other about players they have dealt with.
If the college you do want to go to asks the coach from the college you forgot to respond to, they may tell them that you never even responded to the questionnaire. This makes you look bad in two ways. One, you appear irresponsible. Two, they believe you have no interest in college and in turn mark you off their list. Either way, both results are not good.