Leave the Whisper filter material in the tank for a couple of weeks, then you can remove it. Bacteria doesn't take much time to replace what's been lost by cleaning the filter.
As for the water pH, you don't need to worry about it. Just follow a sound water change routine. By removing and replacing most of the tank water weekly, you'll be able to maintain a steady water chemistry.
"Fear not, my young apprentice. Just change the tank water."