More info will help us give better advice as there are lots of differing ideas on what is the "best" for growing plants. Also there is a really wide range of ideas on what we each may like in appearance, so some of the reasoning will guide us better.
For the basic question of what happens if we do change out the whole, it is true that we will lose some good quantity of the bacteria which may be living on the surface.
But how that changes the overall operation of the tank will depend. Some factors are how quickly you change it all, can the tank handle a bit of increase in bio-overload if you do a few more water changes, as well as how the current fish may react. The loss of bacteria will not be a huge, long drawn out affair like first cycle is, due to it grows back much quicker than having to totally start new.
But I might throw in an idea to save much of the grief/work/worry involved in a total change. If only wanting better planting conditions, perhaps adding to the existing will get what you want? Depending on what you want the end appearance to be, perhaps a mix of existing with added will get you there pretty easy as adding can be done in a way that spikes or much extra water change won't be needed.
I like the look of a mix on the bottom as that is what I'm used to seeing on creeks, rivers and lakes, rather than the one color, solid look. I started with Flourite, found it not to be bright as I wanted, so added a light colored pool filter sand and it gradually became mixed along with several other items like dirt from spilled pots and gravel. I have never totally changed out my sub, but just added more of what I felt right at the time.
Drain the water down, cut the bottom off a soda bottle, fill with the new and when you stick it down into the bottom, you can control where and how much flows out. If it fits what you want, it can be done without any worry or even stirring up too much dust if you work slowly and never add too much at one time.