If more than one person in an ArcGIS Online organization attempts to update a configurable application, their submissions will overwrite one another, even if they edited two different portions of the configuration. Case in point:
8:30 am - Account A logs into ArcGIS Online and updates configurable parameter messageABC in Application X. Saves changes. Minimizes browser window.
9:00 am - Account B needs to change feature layer and fields in Application X. Account B logs in, makes changes, and saves configuration around 9:15 am
10 am - Account A finds out there was a typo in parameter messageABC in Application X. Restores browser, looks at tab where Application X is configured, and updates messageABC. Goes on to another tab in his browser.
11 am - Account B logs in after receiving complaints that users aren't seeing changes to Application X. Account B looks at app configuration, and sees app pointing to original feature layer, and all her changes overwritten. However, messageABC looks lovely. Account B reconfigures app to point at new feature layer, and saves changes to Application X.
What I'm proposing is some sort of notification system baked into the configuration pages that prompts you to accept application configuration updates as they are worked on concurrently by other users, even if they are logged in under the same account. It would be like Google Doc's concurrent editing, or something to that affect.