Setting up an aquarium anew while it is in operation

I own a 180 liter aquarium which has now been in operation for about half a year. I now want to redesign it completely. That means replacing most of the bottom material, gravel, plants, etc. I intend to save about 100 liters of the momentary aquarium water in buckets for refilling the aquarium after the new setup, I will then top it up with fresh tapwater. I will possibly lose many of the bacteria since I will be taking out the entire bottom ground and gravel, and the filter will be switched off for about 3 hours. I want to compensate this with the old water at least to a certain extent, as I must put put the fish back into the aquarium immediately afterwards. Do you have a better idea how I can handle this entire task? I will keep the fish in large buckets while carrying out the new setup. The internal filter is firmly installed inside the tank, I can therefore not just keep it in operation, e.g. on a bucket.