That's weird, I checked all of my all of mys saves, since I started this game at 0.3, check all the saves, from there to 4, and they all, except 2 that were a h scenes, but everything works, i do remember that i did a save of 0.4 content in the 0.5 version and that did get an error, don't know if saves specifically made in 0.5 are errored
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I just found this last week and was still going through 0.5. My save file loaded just fine when you released 0.6.
At the end of 0.6 there is a bit about the paid members and some other stuff. I'm guessing you removed that from the end of 0.5 and put the new content there. If the save is in the middle of that, then it wouldn't be able to load it. Reload it in the 0.5 and scroll back some.
One of the other games I follow in the same system has some problems some times with updates. They suggest that you make multiples saves from different locations when that happens and see what loads.