Actually, saves aren't compatible across versions, so unfortunately you'll have to restart after each update. But you can type commands in-game to get back to where you were quickly. The list of commands can be found on our Discord server, but if you don't use Discord I can send you a PM.
To answer your question, it depends on what OS you play the game. If you play the Windows executable, the save should be at C:\Users\(username)\AppData\Roaming\Godot\app_userdata\Helixteus 3