Hi Steve
Tip 1: Delete protect your apps, maps and data. Use the Delete Protection setting you can turn on for any item you own or have edit access to. You can delete protect the item for your story map, and the items for other components like web maps and data layers. This will protect them from being accidentally deleted by you, or anyone else who has edit access to them (such as your Organization admin). To delete protect items, open their item page in ArcGIS Online or your Enterprise Portal and click the Settings tab. (You can't delete protect story maps from "My Stories" on the Story Maps website).
Tip 2: If you have a lot of content, organize it into folders. Use folders in your ArcGIS Online or Enterprise Portal 'My Content' to organize the web maps and layers used in particular stories. For example you could make a folder for a particular story, and move all the items for that story, including the item for the story itself, into that folder. This makes it easier to keep track of your items. For example, I just use the root (top level) of My Content for testing and other misc items that I don't need to keep, and I occasionally delete those items to clean up. Anything I want to keep longer term I move into a folder, named after the particular story or project. You can rename folders now in ArcGIS Online too. Note that folders aren't reflected in "My Stories" on the Story Maps website: My Stories shows you a flat list of your story maps, irrespective of how they are organized into folders in your ArcGIS My Content.
Tip 3: Use My Stories. The "My Stories" section of the Story Maps website gives you a view of your ArcGIS Online content that just shows you your story maps. You can expand the entries to get a listing of the content they reference. My Stories automatically checks the content to see if it exists and to check it is shared correctly to match how you have shared your story map. So it is a very useful dashboard for story map creation and maintainence. My Stories is also available as an app in ArcGIS Enterprise Portal, so you can also use it if you are using ArcGIS Enterprise instead of ArcGIS Online for your online GIS (see this blog post for details).
Rupert
