This has been officially patched. You can now rearrange your artisan layouts without fear of losing your progress upon re-entry. Context: What’s New in Version 1.1?
: Make use of the game's multiple character and backup slots. Before completing massive endgame transitions—like completing the Lake Temple Altar or building an Attraction—manually back up your profile to safeguard your progression. Coral Island Update v1 1-1223-TENOKE
Here are some of the key features of the Coral Island Update v1.1-1223-TENOKE: This has been officially patched