Hello. Best city generator I've found! Is there a way to save modifications for later work? For example, if I want to add more landmarks later down the line. The permalink just gives the base city and doesn't save any warping or other modifications.

Also, in the "Settlement" menu, under "Points of Interest" what does "Load" do? I looks for a json file but it doesn't seem to actually upload anything, not even landmarks.

No, for now you can only save permalinks.

You can load a precreated (in json format) list of landmarks. It's an obscure way to populate a city with points of interest, but not to restore a modified city.