Well regardless of the cycle and the bacteria, moving your fish to another container, draining the water, adding new water, treating the water, trying to match the old as close as possible especially when it comes to GH, KH and pH is simply going to stress your fish out so bad that I wouldn't doubt it if they didn't live long.
And yes, 100% water changes will cause the bacteria to die if they are left uncovered for any amount of time, starting in as little as 5 minutes and maybe faster if the tank can dry out at all. Even a 50% water change can cause bacteria to die if the water level is left low enough for 5 minutes or more. The bacteria simply dry out and die in short order. I had one of my AC HOB stop running for less than 30 minutes and it caused a major mini cycle.
As long as everything stays wet and has circulation to bring oxygen to the bacteria you are ok but with 100% water changes you take away all the oxygen from the lower bacteria in the water and take away the water that will kill the upper bacteria if the substrate dries out at all. This doesn't even account for the bacteria lost off all the ornaments, the sides of the tank, the intakes of the filters and everything else in the tank. Add a really hot day and the bacteria die even faster.
Not a good idea to do 100% water changes unless you are talking about having the water ready, GH, KH and pH matched to the tank water and temperature as well as dechlorinated and ready to go right back into the tank. If you can do this in less than 5 minutes, I say have at it. 100% water changes done the right way are better than 50%. I for one will stick to my 50% water changes so the filter can keep running and I never have to worry about any more bacteria dying off than needed.
The reason I know the bacteria die fast. I completely emptied a tank once. Removed the fish and put them in another container. Gravel vacced as much as possible to clean the tank and even tilted the tank to get as much water out as possible. Refilled the tank and had everything up and running in less than 30 minutes. The results were a huge ammonia spike and having to recycle the tank for 3 weeks before the ammonia and nitrites went back to 0.
Yes I did it in less than 30 minutes, 26 minutes to be exact because I timed it. I figured if I did it in less than 30 minutes I wouldn't have to worry about a cycle. So much for that theory.