Is money gained from obtaining airline ticket price differences, as a result of personal searching outside the scope of usual work, permissible or forbidden? If it is forbidden, how can it be returned to its owners without harming one's job, and does stopping this action negate the obligation to return what was previously gained?

It is not permissible for an agent to take the price difference for himself without the permission of his principal. Your performing additional work does not make it permissible for you to take this difference for yourself without the company's knowledge. Rather, you may agree with your company to take a fee or commission for this work. You are obliged to return what you have taken to the company, unless its owners legitimize it for you. It suffices for you to return it to the company by any suitable means, even if you fear misunderstanding.