As Randy mentioned...you will rarely see them eat the aptasia...but it should 'disappear'.I have one of those file fish and he eats all the food I put in there and I havnt seen him eat an aptasia yet...
When you say, that you 'have one of those file fish'...are you sure of the species? There are similar 'looking' file fish, that do not seem to ever eat aptasia...maybe post a pic of yours