Interesting. I'll have to do some testing on my end. The next update was supposed to be a major overhaul anyway that would have nuked any previous saves (you can see what's coming on our Discord). I was thinking of ways of integrating old saves, but if this is true, might as well have a clean slate on the new version of ren'py.
The benefits of 64-bit and some of the rendering enhancements outweigh some of the work needed to regain the progress in this case as the game is still light on content.
Either way, lots of testing and dev time to go :D