To answer your question Steve, obviously replacing the substrate is removing a host of bacteria...but the nitrifying bacteria is to my mind rather irrelevant in a planted tank so this is not an issue. The other bacteria which is essential to a stable biological system will also be depleted, along with the organics in the substrate, but that type of bacteria is very fast to reproduce, about 20-30 minutes compared to 20 hours for the nitrifying. Which is why the "other" bacteria has an advantage.
When I've done this, as I have with 5 of my tanks in the past year, I keep the wood and plants from the tank wet, usually in the temporary tank with the fish, and once the new substrate is in, I half fill the tank, dechlorinate the water, and move over the wood to aquascape, then the plants. There is bacteria on all these surfaces, which may or may not come into play with all the live plants. And I also use new or tap water washed filter media when I do this, which removes all of that bacteria too. My last reset was the 115g with 90+ fish that all went in the first day, and not one issue. The plants will usually be more affected because the lack of organics removes a lot of nutrients, esp CO2, until it rebuilds.