What I'm suggesting is to follow standard WP design as other parts of the system do and use this red circle counter on the main menu. Whenever there are unsynced field groups a count of them would appear in such a circle next to the ACF main menu item.

It's really important to keep field groups in sync, failing to do so can cause lots of confusion and lost time. This would make it instantly clear to a dev that the site is out of sync with the json files.