No it should not hurt the fish, they can take it. I have heard of people saying to run carbon and it will help clear up the cloudiness or I prefer changing the filter floss because it can get clogged with the silt, which is still good silt, but it should not be clogging your plumbing or filters. So keep them clean.
Keep and eye on the ph, all new aragonite sand can have an effect on the ph.
Thomas