The current problem with the game is, that most of the state holding variables are not recognized by Ren'Py, so they are not saved and will be set to their default values on savegame load. For examples the $skills array does not show up in the variables viewer (Shift+D > Variable Viewer). From playing and reloading a fresh save I can say at least skills, the province improvements and decrees are not saved.
Changing the definition of that skills array from "$skills = [ ... ]" to "default skills = [ ... ]" solved at least that issue. I did not bother to check if that works for other variables too.
Changing the definition of that skills array from "$skills = [ ... ]" to "default skills = [ ... ]" solved at least that issue. I did not bother to check if that works for other variables too.