We are still investigating the issue. It's taking longer than expected as we are having trouble reproducing the bug on our side. While we continue to work on the issue, would you like to try to delete and reinstall the game and see if that would fix the issue?
Please keep a copy of your current game ID before reinstallation.
If you have saved the game with your Google Play /Facebook/Kongregate account, you will be able to get back your progress including the amethyst tree after reinstallation. You might need to go through the new player tutorial before the game gives you a pop-up asking you to choose between a LOCAL or CLOUD saved data. When you see that please go with CLOUD.
If for any reasons you are having trouble getting back the progress after reinstallation, we can use the game ID (mentioned above) to do a manual account configuration on our side to retrieve the data.