I wouldn't start with all new substrate. If you want to replace some, it's a different story, but IMO it wouldn't be beneficial in anyway to replace all the substrate. You'd be removing beneficial bacteria.
Although, yes, it would remove beneficial bacteria; that is more or less a non-issue most of the time. It might make a difference in a minimalist tank or a heavily stocked tank, but the typical amount of rocks themselves are more than enough for the average bioload.
However, there are risks in keeping the old substrate. Once you drain the tank, and start stirring the sand, you are going to kick up all sorts of gunk. Some of which could be toxic or nitrate heavy. I have always started with replacement sand (ideally used sand, new just takes so long to rinse and cure...).
Then there is the matter of logistics. The sand comes out last but has to go in first(ish); how are you going to do this?
Now, @OP has multiple tanks, so I would consolidate one tank to the others, drain until about 3-4" from the bottom. Store the rocks in a bin temporarily. Stir the bed, releasing all the toxins and gunk, drain the tank and discard the gross water. Rinse the sand with some of the clean water; there you go, live and clean substrate! Rinse and repeat for each tank (pun intended).
I would also get the temporary bins cycling as soon as possible, which may or may not be possible in this situation. At the very least filled with water (up to temp) and a few rocks...
Watch for ammonia for the first couple days after moving the system and keep some Prime on hand, just in case...