i did this when switching from gravel over peat moss to mts capped with pool filter sand. i just saved 50% of the water and put the fish in a bucket, pulled up all my plants, and hosed out the mess, and added a whole new one haha (not really, i rinsed the pfs thoroughly so no cloudiness). i then put the saved water in, then planted, then the fish, then filled the tank. not a single problem. took me maybe two hours total.
if you are worried you can get some bacteria to add to the tank to replace the lost ones.
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