The Tropica growth substrate should be sitting rather like a mud layer on the bottom of the tank, but you may see clouds of silt/fines released into the water column as you remove plants & again as you remove the Manado
Before starting this process, I do daily water changes for a few days so that tank & tap are well matched, then if I need to do extra water changes during the plant & substrate removal process, tap water is very similar parameters
I also add additional Seachem Prime (it's quite decent at binding nitrogenous compounds) during the process (I dilute the Prime into tap water before pouring into tank)
When removing plants, I turn down the filter flow & hold syphon close to whichever plant I'm pulling out - so that released dust etc goes out to my water change bucket
Once water level drops to 50 - 60%, I refill tank (adding double dose Prime) & allow filter to run for 15-20 min
Then repeat process - pay attention to shrimp, if they act stressed, need to re-evaluate your process
Once plants are out, it's easy to syphon out the Manado etc
I find that moving livestock (net them slowly without any "chasing") to a quiet temporary tank is less stressful (to me) & apparently them
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I have the temporary tank prepared with ~ 50% tank & 50% tap water, water movement, heater etc, dim lighting, some leaves or wood for hiding areas ...
This way I can take as much time as I like for the rescape
I suppose it depends on how much substrate/plants you need to remove, how clean your sand is (that you'll be adding to the tank) - some fish are much more stressed by activity in the tank than others.
Or should I top manado with sand, disturb manado and sand will go down and cover Tropica substrate and after that syphon manado out?
I don't think this will work very well in practise