Hi,
There should be no problem with retaining save files between updates.
On PC save file is kept outside of the game folder, which means that you can freely download new update, unzip it, and play.
On Android its slightly different, as you need to download the update and install it WITHOUT deleting the current version - this will trigger the "Update" pop up. Otherwise, if you delete old version - you'll also delete save data.
Cheers