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Yeah it is a little stressful on the fish, you are destroying their territory and if you are using sand and it makes the water cloudy it gets hard to see where the fish are. I have done it a few times and I have to be careful not to put the rock down on a crab or snail
The cloudy water will clear up in a few hours. Try not to stir up to much since I can affect your water parameters (nitrate, ph, etc)