That might work but I'd worry about the beneficial bacteria (often aerobic) not being able to thrive/survive deeper in the substrate where the anaerobic bacteria would normally stay (low oxygen and water movement)
Also, where will you keep your fish during the process? If in another (uncycled) tank than the water would need to be changed in large amounts very often to keep the ammonia levels down
A way I'd read to change substrate is a little at a time using plastic dividers. Remove about 1/4 of the substrate (top to bottom) from the tank at a time using the divider to keep them from mixing. Replace the substrate you removed with the new substrate and let the tank run a week or so so your beneficial bacteria colony can populate the new substrate. Then do the same for the next 1/4 of the tank, etc, etc until the substrate is (very slowly) replaced by the new substrate. Slow is better as it'll allow the new bacteria to help populate the bacteria colony over time
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