While your situation is regrettable, my feelings on this matter are polar opposite and I'm actually glad that PG went this route.
Just like Renpy games, even if I delete Lisa after playing it, my saves are safe in my directory profile and are reacquired after each new update.
Now don't get me wrong, I'm not implying that you should "quit whining and deal with it". I just wanted to drive home the point that no one solution will fit all. That being said, if I may offer an unsolicited advice, I do have a suggestion:
While there are multiple solutions, but since you mentioned having an unstable system, my suggestion for you would be the following:
- Play the game and finish it.
- Head to your profile C:\Users\YOUR USERNAME\AppData\Local\User Data\Default\Lisa
- Zip up your save folder and head to this thread.
- Leave a random message and attach the save.zip folder here.
Since most save folders are below 10mb threshold, you should have to little to no issues pulling this off. And voila, your very own save backup on the internet in the very thread where you track Lisa's progress. Next time, when you come by to play the newest build, just make a search for your name on the thread and you will jump right to your own reply with the saves.
While not the best solution, I do believe it's the least intrusive and most viable for your particular scenario where you constantly loose access to your local data.