I don't fully recall the whole thread and maybe I should read it again. But I created a thread regarding water changes and beneficial bacteria. In that thread I pretty much prove that in the case where your source water is suitable, there is no negative impacts to bacteria even at 100% water change.
As far as different filters go, it won't make a difference to the bacteria so long as the media is suitable for growth and conditions are favorable.
Most important thing to understand is this: if after performing a large water change has some kind of negative effect on your fish it's very likely due to the source water and nothing to do with the bacteria in your aquarium.
Also note that even if you completely wiped out the cycled media, it would not cause for an immediate death or reaction from your fish. Ammonia or nitrites are not going to magically spike. It's likely untreated tap water or a huge temp swing or supersaturated gasses or toxins in the source water.