Overwriting a hosted feature service after the service definition file and feature service have been moved out of the root folder (to custom folder), saves a new service definition file in the root folder instead of the new custom folder.
Non-reproducible in the November 2015 Online release (3.10).
対処法
1. In ArcMap, instead of overwriting, create a service definition file, and save the file locally.
2. Click the service definition in ArcGIS Online located in the custom folder, and view the item details.
2. Click Update > Update, and update with the new service definition file that was saved locally.