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There's no point adding stress to your already stressed-out upper respiratory system, and that's what the change in air pressure will do. Flying with cold or flu congestion can temporarily damage your eardrums as a result of pressure changes during takeoff and landing. If you must fly, use a decongestant and carry a nasal spray with you to use just before takeoff and landing. Chewing gum and swallowing frequently can also help relieve pressure.
You put a salt and warm water mixture in something that looks like a little teapot. Then pour it through one nostril and let it drain out the other. You have to practice a little, but once you get the hang of it, it can ease allergy or cold symptoms and may even help you get rid of a cold quicker. Just make sure you use distilled or cooled boiled water and keep your neti pot clean.