The only update that has been done that could affect the game saves is on Linux, where the saves folder has been changed for Steam Cloud... if you play on linux then I can help you, otherwise it must be some internal bug, I would need information, the logs folder and the saves (on windows it is inside appdata/roaming/toziuha...).

I was playing on a steam deck. For what its worth I've gone past that point in the game now and this has not happened again.