Are you swabbing out your flute before you put it away? Hopefully so, it is critical that you keep your flute clean inside and out. But what are you using to swab out your flute?
I advocate using a simple, 100% cotton handkerchief or bandanna. They are absorbant and nonabrasive, readily available and inexpensive. Cotton works great for wiping off the tenons so the joints go together smoothly, too. Cotton is also washable so when it gets grubby, just throw it in with the regular laundry (using fabric softeners may not be a great idea, though). Very practical!
A silk swab is nice, but it can be fragile and tends to flatten out after a couple of uses. A 10″ or 12″ bandanna or kerchief will stay full enough to clean the whole tube for several uses. You could just use a strip of cotton or a square piece of cotton, but I think the edges should be finished so stray threads don’t get caught in the mechanism.
As for the fuzzy flute swabs that are so popular, I do not recommend them. They are supposed to “wick the moisture away from the pads”. Great! But what do you do after you have done that? You stick it right back into the flute! Where is the moisture supposed to go? I live in Florida and any moisture that is allowed to sit around leads to one thing, mildew. While I haven’t heard of too many cases of “flute mildew”, I do know that once you get the moisture off the pads, you should keep it away from them. If you feel you have to use the fuzzy things to swab out your instrument, fine, but do not store them in your flute or inside your case. Besides, you will still need a soft cloth to wipe off the joints and the fingerprints, so why not just get a cotton cloth or two and leave the fuzzy things alone. I also suggest that your flute cleaning cloth not be stored inside the case with your freshly swabbed out flute.
This is all part of good flute maintenance, which results in better flute performance. It’s easy, it’s practical and it’s cheap. Besides, you can create a collection of cool “flute” bandannas that will make you the most stylish and hip flutist around!