This has happened to me on several story maps and other apps. I will add layers to the map, save the project and when I return to my app or web map after days/weeks of not touching it, it will be missing data. This only happens to layers/services hosted on my organization's server, which is a SQL + ArcGIS Server combo. If lost, the layers will still be running in ArcGIS Server and in "my content" on ArcGIS.com. Has anyone ever this happened and found the cause?