I just got back from an exhilarating four days on Long Island, where I was part of the team that hosted Flute New Music Consortium's New Music Festival at Stony Brook University. I don't know if it was the stress of the festival, the lack of sleep and poor eating habits while I was there, all the time spent walking around campus in the bitter cold and gale force (really!) winds and sitting on trains and planes, or just because it's winter, but now that I'm home I am S-I-C-K. Like, almost Coronavirus level. And I am now remembering just what an inconvenience illness is when you do something as physical as playing the flute for a living. So, whether your illnesses are weather-related, stress-related, or come from filthy people invading your personal space, some thoughts on how to get through it when you're past the point of prevention:
Hydrate, hydrate, hydrate. Think of this as prevention AND remedy. Herbal tea or just hot water might be more comforting than cold water if you've got chills, drainage, or a sore throat. (I am drinking hot water all day now.)
Invest in a personal humidifier or vaporizer. The more moisture you can add to your immediate environment the better.
I'm not going to tell anyone what drugs to use, but find a decent decongestant, pain killer, and cough suppressant that you can live with. I avoid drugs whenever possible, but now is not the time to be a hero if you've got concerts coming up.
Be a baby. Sleep, lay around binging on Netflix, do what you've got to do to conserve energy and let your body heal. A couple days of missed lessons is less expensive in the long run than a lingering cough that hangs you up for a month.
Staying in shape on your flute: probably not totally going to happen, but there are a couple things you can do so the transition back to playing isn't as painful. Whistle tones will give your embouchure something to remember when you can't spare the air speed to play fully without having a coughing fit. And if you have a lot of notes coming up, you can always practicing the "typing" without blowing into the flute. Play along with a recording if you're up to speed, or woodshed with the metronome on the body of the flute.
Once you get back into practicing, you may have to rebuild lung capacity (I always have to). Moyse De La Sonorite, pp. 10-14 are a brutal but very helpful boot camp.
Take care of yourselves this winter! But failing that, know it's temporary, and baby it so you can get back in the saddle as soon as possible.