Hey Tyler. I didn't do a complete substrate change, but when I first setup my 75g, I bought fish the same day. I set everything up and moved an already established filter to the 75g and squeezed one of the sponges directly into the water. You should see all the bacteria and whatnot cloud up your water. I let my filters do their thing and once the tank water was clear again and the temp where I wanted it, I acclimated my fish and put them in with no issues.
I think you should be fine moving your fish to a container, switching your substrate, running your filters for an hour or two, and then reintroducing your fish. It wouldn't hurt to add the old water either. Although, most of the beneficial bacteria will be on your decor and substrate, not your water. But hey, it couldn't hurt so why not. Just be sure to check your parameters for at least a week to be safe. Hope this helps!
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