Kate -- Glad things are working as expected now. Not adding -modified shouldn't make the app unstable. Just make sure you are careful about the order in which you make edits and save them if you have the builder and AGO Assistant open simultaneously.
For example, if you load the story JSON in AGO Assistant, then make changes in the story map builder without saving, then edit and save the JSON, your changes from builder would be lost (since you loaded the JSON before they were made). After saving changes in builder be sure to click the item name in the left column while viewing the JSON in AGO Assistant to request the latest.
Owen Evans
Lead Product Engineer | StoryMaps