Many chunks get replaced when upgrading an old world

Almost every time I try to update a world to any version that has the Caves and Cliffs world generation, many chunks get replaced by new ones. It shouldn't be a really big problem but it also deletes chunks with builds in them. It is especially noticeable with pre-1.13 worlds that shouldn't have algae and with old beta worlds that have a different water level so sometimes it's like an ugly checkerboard with water at y63 and y64 not mixing smoothly at all.