When you’re done playing, are you quitting the game or just closing the window?
It seems like some parts of the map are only saved when the client itself is closed. If you just save and quit the character, then close the window, you may not be saving everything. Not 100% sure what the does, but I’ve just learned not to do it.
Basically, when you’re done playing
Shift + S to save and quit
At the main menu, scroll down and quit the game gracefully