How many liters are you using in your system? Are you using any AF Life Biofil or just Siporax?Nope, two dips in freshwater will not kill any bacteria. Still if they do they can grow back up much faster than we can imagine. Dont underestimate the power of bacteria....lol. Actually they are always dying and regenerating in your system so dont worry much. My cleaning is due this weekend so I will show you how that water looks like after 2 dips. Also they grow a lot of sponge in them.