There's probably not a right answer to this. The dev improves and changes a few things here and there. Old saves will most likely break up or cause problems. That's the nature of wip. What I say now is not meant to be an insult but perhaps some of that stuff could be avoided if the dev would have more experience with the engine and overall mechanics.
It's a learning process for him too after all. So basically expect more stuff to not behave as it should in the future. If
Amorous Dezign always provides a fresh save and walkthrough for the new content of each build the frustration should be at a minimum.
