I drop my water level by about half every spring. It gets rid of the nasty dirty water and replenishes it with healthy oxygenated water. (I know bad water will kill fish because I've seen it happen enough in a goldfish bowl.) I don't clean the walls because I don't want to see a nice clean new looking liner. As far as the bacteria goes who knows? Supposedly it doesn't grow in the cold so that tells me it has to start fresh every year. There is a lot of information on the internet that gets repeated but unless I have personal knowledge I can't say one way or the other. I'm the first to admit I'm not a marine biologist or chemist.
I tend to do this as well. It doesn’t matter how much fall cleaning I do, or how many nets I put over the pond, by late winter my pond will be filled with massive amount of leaves leaving the water brown and nasty. Not sure if it’s due to living on top of a hill where all winter winds are whipping everything around but I will empty half if not more just so I can scoop out the mountain of leaves. Then refill using my well water. Crystal clear water and the fish seem happy so....