If the floss is your only filter medium, then removing it will remove your only source of biological bacteria. You should keep/seed some floss in your DT, so that you can pop in newly-seeded floss when you remove the old floss from your HT. In the meantime (until you have seeded floss ready), I would just rinse the dirty floss in some removed tank water when you do a WC and keep it in the HT for now.