I'm very sorry you lost your save. It was unfortunately a much needed change, as the old saving system was bringing a lot of issues. This new system ensures every save file from now on will be safe, no matter how much I update the game
If you want me to, I can create a new save file for you. Just let me know roughly what upgrades you had and which Pokemon you've unlocked, I'll send it over. Alternatively, if you created a new one, I can modify it to include your old progress.