Let me try to understand. Your main tank is now empty, right? Everything dead?
Either leave it fallow for two weeks without thermostat and then do a major water change or empty it, bleach it, clean all the media and start again.
You acn also, withou fihs, throw in potassium permangananet and leave it for a couple of days.
Water will turn res, whilie it is oxydizing everytning, the good and the bad, and then start again fom scratch.