I just throw it away. I bag can last me a whole year so I really don't bother with trying save it. Its more important to me to keep the nutrient level down. See if you let water wash thru the waste that the floss collects this leads to and increase in nitrates in your aquarium. An it is best to limit the increase and control it by measures like throwing away floss. We see the rise of these roller mat devices that advance as they clog up with the waste to do the same thing. If you travel for work or have the money and space to install such a device it nice. I have the 5 minutes a day to do it so I just replace the floss. It's part of keeping the nutrient input of the tank under control. This along with a measured feeding of the fish keeps me from having to deal with over nutrient issues like cyano hair algae and the like. It has taken me a long time to learn this.:) An I have to learn it a new with each new tank I set up. As each tank will have slightly different limits to which one can work with as far as the input of nutrients and what methods are needed to achieve a balance for the input of the nutrients. If you have a large aquarium say 500 gallons you can get away with a lot. As you have water volume on your side. In a small aquarium you can not get a way with anything you must have a very strong removal of nutrients or you will be fighting issues of water quality all the time.
