Edits that have been made in the Settings Tool are not saved automatically.
The Apply button in the bottom-right corner needs to be selected before closing the Settings Tool for any changes to persist.
If you are still unable to save your edits, please let me know.
Please see: Sometimes I can't scroll down in the Properties tab. for a similar issue.
This is a known issue and a high priority for the next release of AppStudio for ArcGIS (BETA).
The only workaround at this time is to use the Settings Tool when your are not signed in to ArcGIS Online.