Personally I think he started this chapter with clean slate (you can even change your name) so it just assumes that you finished all scenes from the previous 2 chapters, which is pretty sensible considering it almost feels like a different game.
I tried different saves and starting new and a lot of the functionalities doesn't work properly (as he stated in the previous post), but it all plays the same. So maybe don't delete your previous version and just treat it like another separate chapter that starts fresh.
Maybe it's because as the development progresses he wanted to do much more than the original frame can handle, remember we had an UI overhaul once already, but the story so far seems to indicate another holiday island situation where all the events in the new setup is somehow separate from the yacht. I hope we can get some sort of an open map system including all the bits from previous versions so the story can probably flow without the constraint we have right now.