Yes it will severely muck up the water during a heavy uprooting.
Part of keeping a healthy tank healthy is learning to grow the right plants under the right conditions, so you don't have to do a lot of substrate damage.
If you must do a lot of that, do it at various times, not all at one time, do a little each day.
If your prone to making a mess regularly a diatom filter would be a nice investment.
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