CFC makes a good point, if the replacement water is different from the old tank water. If and only if, you can match the pH, the hardness, and the temperature of the new water with the old, the fish would not suffer too much shock. But, if you have to sit the fish in a bucket for too long while the temperature equilibrates, you'll do more harm than good. 50% each day for several days is the much safer route.
But, also in response to your question about the bacteria: more of the bacteria are sessile, that is not mobile, and found on the surfaces of your tank and filter. Taking out the water will take out an insignificant amount of bacteria. So long as you don't allow the tank surfaces & filter surfaces to dry out, the bacteria will remain active.
Maybe if you expound upon "a water issue" we could give more specific advice. "A water issue" means a lot of different things to a lot of different people.