Hey, all 3 issues you mentioned are the direct result of the game simply not being finished lol. I already addressed the first two issues in the next update coming in a day or two, and the third one, well, it's just a question of data type which I can fix in seconds. Thanks for playing to the end!
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