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?
Thanks,
Charlie