Updates won't affect your saves that much (i even want to say that they never affect your saves), except for updates that change game structure itself (like 0.42) - game would ask you to "fix" the save if it's old and need to be adapted to the new version of the game. Btw i think there is a generation problem (like in Minecraft) like you studied this part of terrain, updated the game, there added new biomes for example, you went into the unstudied places and boom! Suddenly, generation there is seems to be odd if compare to old generation.