I was unable to test the new version until now, and I discover like you that the "throne scene save" are bugged so I've edited my save files post with newer versions. All the saves for all the path are now working properly, they just start after the throne scene at the start of the free roam.
You can find all the save files in this post.
Additionally, you can choose the "Paths" button on the main menu; it's now updated and you can start from the 0.5.0 (at the introduction of chapter 3)
If you want to, you can use my end of 0.5.6 in Cecille path save file (Female Erin) that I attached in this post, I just tested it, it's working on my end.
I was able to load this save and see new content.