Switching canister filter safe? or will I loose all my good bacteria?

[lovemybarbs]

I'd worry about the substrate more than the filter.

 

[TookayS2K]

Just to update... my tank started leaking so I had to do a complete reseal. I moved my fish to a temp tank, along with my filter and most of the water. The gnats took over that tank as well.

Now that my tank is resealed, I'm cycling it and going to be moving my fish back. Hopefully I won't transfer any gnats back over. Wish me luck!