Before you blow up, you could have check this forum to see if anyone has experience that kind of issue. Also if you manually do the save in the VN, not only it save in the extracted VN folder, it would also save it in another location in your user profile if you are using Microsoft Windows.
In this case, did you use a Mod last time? Did you make your own backup of your save?
Also it does look like minor mistake with "..\Save\persistent" what I see in the compress download. However the question is is it also in the original download. If so, we just need to let the developer know about that, I am sure it was an honest mistake if that the case. Sometime it may be related to the VN product that there may be an unknown issue that not many are aware of that. Also some of the developers has testers to test it.
There is a trick that you can breeze through to where you last saved, it may take a moment to do it. Believe me, I had done the same thing on number of VN that was not usually the developer fault it has to do with the software update that once in a while will have a minor glitch that disrupts the save file as well the persistent file. The easy solution is to start all over.
Have a good day and be safe...