2500+ hours, many seeds, many bases, never had terrain reset, unlike NMS, where terrain always resets and messes stuff up. That list includes my first base which I go back to on a regular basis. I think you are safe to manipulate the terrain, though it is one of the things that can cause lag if extensive. This is solo, in co-op it also doesn't reset but definitely causes lag, not as much as a year ago, but you will notice it if you choose to Build Big or if multiple players build close to one another.