Our bathroom toilet overflowed and poured down the floor air vent. We noticed after a few weeks that no warm air was coming out in that room. We discovered that the tube running to that vent was full of water. We took it down and blocked up the hole the tube used to be connected to. The next morning we discovered there was no warm air blowing out anywhere. I turned off the furnace. Tried it again later and it was warm for a little bit, but soon stopped being warm again. Is having that tube disconnected make the furnace not work properly or is just a coincidence. We plan to replace the tube with a dry one.

Is this an electric or gas furnace?

The rest of the home is heating OK, right? Tube? Is this a flexible air duct? Air -  www.ducting.com If so they can sag and create a type of trap like under your sink. Look for low spots and pierce with a nail