Personally I would tell them about it. What's the worst that could happen? Yes They might turn your application down because you have been honest or they might see your honesty as a quality they want in a pilot working for their company and take you on. A far worse scenario would be that they accept you and you get you excited, turn your life upside down in preparation for starting the course only to find it has shown up once they perform a background check on you and see that you haven't been honest and cancel your offer?
In any job interview etc honesty is always the best policy
Good luck with the application