Removing the content from out of a <ref> .. </ref> should prompt the user that they need to delete the reference. Perhaps a tooltip, or this might be an opportunity to use a hover trick to give the user something to click to acknowledge they intended to delete the ref.
It shouldnt be possible to save with an empty ref, as that is an error condition.
https://en.wikipedia.org/w/index.php?title=User:John_Vandenberg/test&diff=566133128&oldid=566132993
Version: unspecified
Severity: minor
See Also:
https://bugzilla.wikimedia.org/show_bug.cgi?id=50609